Hi, my refinement (Refmac_5.2.0019) in sp. grp. C2 with 2 TLS groups,
bulk solvent, and overall anisotropic scaling gives the following
output:
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-----
Overall : scale = 1.143, B = 0.148
Babinet"s bulk solvent: scale = 0.000, B = 144.972
Partial structure 1: scale = 0.292, B = 32.999
Overall anisotropic scale factors
B11 = 5.13 B22 = -4.26 B33 = -0.52 B12 = 0.00 B13 = 0.64 B23 =
0.00
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Rfree is currently 28% at 20-2.4 A resolution. (TLS parameters shown
below if you're interested)
Two points of mild confusion:
1. Most other refinements I've done have a non-zero scale for the bulk
solvent. What causes the zero scale, and is it something to worry about?
2. If the individual atomic B-factors are approximately correct,
shouldn't the partial structure 1 B-factor be closer to zero, instead of
32.999? Or is its non-zero-ness a consequence of the TLS (and if I
merged the TLS into the Bs, using TLSANAL, then the partial structure B
would indeed be near zero)?
Thanks!
Dave
David Borhani, Ph.D.
D. E. Shaw Research, LLC
120 West Forty-Fifth Street, 39th Floor
New York, NY 10036
[log in to unmask]
212-478-0698
http://www.deshawresearch.com
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 2
REMARK 3 ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 3
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 32 A 341
REMARK 3 RESIDUE RANGE : A 401 A 401
REMARK 3 RESIDUE RANGE : S 1 S 2
REMARK 3 ORIGIN FOR THE GROUP (A): -32.4343 22.5714 7.0463
REMARK 3 T TENSOR
REMARK 3 T11: -0.5700 T22: -0.5229
REMARK 3 T33: -0.5351 T12: -0.0126
REMARK 3 T13: -0.0556 T23: -0.0074
REMARK 3 L TENSOR
REMARK 3 L11: 2.4138 L22: 5.2360
REMARK 3 L33: 1.4696 L12: 1.7421
REMARK 3 L13: 0.6968 L23: 0.2662
REMARK 3 S TENSOR
REMARK 3 S11: -0.0621 S12: 0.0364 S13: -0.1010
REMARK 3 S21: -0.4655 S22: 0.1014 S23: 0.2989
REMARK 3 S31: 0.2044 S32: 0.0265 S33: -0.0393
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 2
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : B 2 B 161
REMARK 3 RESIDUE RANGE : S 3 S 6
REMARK 3 ORIGIN FOR THE GROUP (A): -27.0203 61.6964 24.9773
REMARK 3 T TENSOR
REMARK 3 T11: -0.7162 T22: -0.4572
REMARK 3 T33: -0.7055 T12: 0.0704
REMARK 3 T13: 0.0110 T23: -0.0653
REMARK 3 L TENSOR
REMARK 3 L11: 2.5808 L22: 2.4723
REMARK 3 L33: 5.5878 L12: -0.1780
REMARK 3 L13: 1.4392 L23: -0.9551
REMARK 3 S TENSOR
REMARK 3 S11: -0.1936 S12: -0.1926 S13: 0.4036
REMARK 3 S21: -0.0774 S22: -0.0593 S23: 0.1368
REMARK 3 S31: -0.4974 S32: -0.4284 S33: 0.2529
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