Starting phenix.real_space_refine
on Mon Jan 20 11:05:48 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/9btu_44896/01_2025/9btu_44896_trim.cif
Found real_map, /net/cci-nas-00/data/ceres_data/9btu_44896/01_2025/9btu_44896.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.68
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/9btu_44896/01_2025/9btu_44896.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/9btu_44896/01_2025/9btu_44896.map"
model {
file = "/net/cci-nas-00/data/ceres_data/9btu_44896/01_2025/9btu_44896_trim.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/9btu_44896/01_2025/9btu_44896_trim.cif"
}
resolution = 3.68
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
qi {
qm_restraints {
package {
program = *test
}
}
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= 0.001 sd= 0.010
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 5
Type Number sf(0) Gaussians
S 61 5.16 5
C 4948 2.51 5
N 1321 2.21 5
O 1531 1.98 5
H 6422 0.53 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 14283
Number of models: 1
Model: ""
Number of chains: 10
Chain: "B"
Number of atoms: 6644
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 424, 6644
Classifications: {'peptide': 424}
Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 402}
Chain breaks: 1
Chain: "D"
Number of atoms: 575
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 115, 575
Classifications: {'peptide': 115}
Incomplete info: {'truncation_to_alanine': 115}
Link IDs: {'TRANS': 114}
Chain breaks: 1
Unresolved non-hydrogen bonds: 230
Unresolved non-hydrogen angles: 345
Unresolved non-hydrogen dihedrals: 115
Planarities with less than four sites: {'UNK:plan-1': 115}
Unresolved non-hydrogen planarities: 115
Chain: "C"
Number of atoms: 6484
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 413, 6484
Classifications: {'peptide': 413}
Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 395}
Chain breaks: 4
Unresolved non-hydrogen bonds: 36
Unresolved non-hydrogen angles: 43
Unresolved non-hydrogen dihedrals: 31
Unresolved non-hydrogen chiralities: 2
Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1}
Unresolved non-hydrogen planarities: 18
Chain: "E"
Number of atoms: 365
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 73, 365
Classifications: {'peptide': 73}
Incomplete info: {'truncation_to_alanine': 73}
Link IDs: {'TRANS': 72}
Chain breaks: 3
Unresolved non-hydrogen bonds: 146
Unresolved non-hydrogen angles: 219
Unresolved non-hydrogen dihedrals: 73
Planarities with less than four sites: {'UNK:plan-1': 73}
Unresolved non-hydrogen planarities: 73
Chain: "A"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 9
Unresolved non-hydrogen chiralities: 3
Chain: "H"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 9
Unresolved non-hydrogen chiralities: 3
Chain: "I"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 9
Unresolved non-hydrogen chiralities: 3
Chain: "J"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "B"
Number of atoms: 42
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 42
Unusual residues: {'NAG': 3}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 9
Unresolved non-hydrogen chiralities: 3
Chain: "C"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Time building chain proxies: 8.43, per 1000 atoms: 0.59
Number of scatterers: 14283
At special positions: 0
Unit cell: (109.858, 94.164, 118.944, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 5
Type Number sf(0)
S 61 16.00
O 1531 8.00
N 1321 7.00
C 4948 6.00
H 6422 1.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=17, symmetry=0
Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 272 " distance=2.03
Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 189 " distance=2.03
Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 203 " distance=2.04
Simple disulfide: pdb=" SG CYS B 249 " - pdb=" SG CYS B 256 " distance=2.03
Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 448 " distance=2.03
Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 444 " distance=2.03
Simple disulfide: pdb=" SG CYS B 390 " - pdb=" SG CYS B 440 " distance=2.03
Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 426 " distance=2.03
Simple disulfide: pdb=" SG CYS B 401 " - pdb=" SG CYS B 415 " distance=2.03
Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 283 " distance=2.03
Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 214 " distance=2.03
Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 267 " distance=2.03
Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 457 " distance=2.03
Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 453 " distance=2.02
Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 449 " distance=2.03
Simple disulfide: pdb=" SG CYS C 407 " - pdb=" SG CYS C 434 " distance=2.03
Simple disulfide: pdb=" SG CYS C 409 " - pdb=" SG CYS C 423 " distance=2.03
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
Amino acid : True - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Links applied
BETA1-4
" NAG A 1 " - " NAG A 2 "
" NAG A 2 " - " BMA A 3 "
" NAG H 1 " - " NAG H 2 "
" NAG H 2 " - " BMA H 3 "
" NAG I 1 " - " NAG I 2 "
" NAG I 2 " - " BMA I 3 "
" NAG J 1 " - " NAG J 2 "
NAG-ASN
" NAG A 1 " - " ASN B 141 "
" NAG B 701 " - " ASN B 449 "
" NAG B 702 " - " ASN B 364 "
" NAG B 703 " - " ASN B 378 "
" NAG C 701 " - " ASN C 248 "
Time building additional restraints: 3.99
Conformation dependent library (CDL) restraints added in 1.1 seconds
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 1978
Finding SS restraints...
Secondary structure from input PDB file:
33 helices and 13 sheets defined
35.8% alpha, 30.0% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.32
Creating SS restraints...
Processing helix chain 'B' and resid 104 through 128
removed outlier: 5.772A pdb=" N HIS B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A)
removed outlier: 6.351A pdb=" N LEU B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A)
removed outlier: 5.829A pdb=" N ASP B 114 " --> pdb=" O HIS B 110 " (cutoff:3.500A)
removed outlier: 5.852A pdb=" N LEU B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A)
Processing helix chain 'B' and resid 129 through 132
Processing helix chain 'B' and resid 133 through 138
Processing helix chain 'B' and resid 141 through 146
removed outlier: 3.928A pdb=" N TRP B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A)
Processing helix chain 'B' and resid 210 through 228
Processing helix chain 'B' and resid 231 through 236
Processing helix chain 'B' and resid 237 through 239
No H-bonds generated for 'chain 'B' and resid 237 through 239'
Processing helix chain 'B' and resid 241 through 245
Processing helix chain 'B' and resid 257 through 261
Processing helix chain 'B' and resid 290 through 293
Processing helix chain 'B' and resid 302 through 306
Processing helix chain 'B' and resid 328 through 333
Processing helix chain 'B' and resid 372 through 378
removed outlier: 3.658A pdb=" N ASP B 376 " --> pdb=" O PHE B 373 " (cutoff:3.500A)
Processing helix chain 'B' and resid 382 through 400
Processing helix chain 'B' and resid 422 through 433
removed outlier: 3.710A pdb=" N LEU B 430 " --> pdb=" O CYS B 426 " (cutoff:3.500A)
Processing helix chain 'B' and resid 433 through 444
removed outlier: 3.676A pdb=" N ARG B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A)
removed outlier: 4.162A pdb=" N CYS B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A)
Processing helix chain 'B' and resid 467 through 480
Processing helix chain 'D' and resid 61 through 68
removed outlier: 5.742A pdb=" N UNK D 66 " --> pdb=" O UNK D 63 " (cutoff:3.500A)
removed outlier: 3.544A pdb=" N UNK D 68 " --> pdb=" O UNK D 65 " (cutoff:3.500A)
Processing helix chain 'D' and resid 74 through 76
No H-bonds generated for 'chain 'D' and resid 74 through 76'
Processing helix chain 'D' and resid 87 through 91
Processing helix chain 'C' and resid 106 through 126
removed outlier: 4.905A pdb=" N HIS C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A)
removed outlier: 5.719A pdb=" N LEU C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A)
removed outlier: 5.653A pdb=" N ASP C 116 " --> pdb=" O HIS C 112 " (cutoff:3.500A)
removed outlier: 5.574A pdb=" N LEU C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A)
removed outlier: 3.733A pdb=" N ARG C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A)
Processing helix chain 'C' and resid 154 through 158
Processing helix chain 'C' and resid 221 through 239
Processing helix chain 'C' and resid 242 through 250
Processing helix chain 'C' and resid 252 through 256
Processing helix chain 'C' and resid 268 through 270
No H-bonds generated for 'chain 'C' and resid 268 through 270'
Processing helix chain 'C' and resid 301 through 304
Processing helix chain 'C' and resid 313 through 317
Processing helix chain 'C' and resid 390 through 408
Processing helix chain 'C' and resid 430 through 444
Processing helix chain 'C' and resid 448 through 453
Processing helix chain 'C' and resid 476 through 487
removed outlier: 3.697A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A)
Proline residue: C 482 - end of helix
Processing helix chain 'C' and resid 497 through 499
No H-bonds generated for 'chain 'C' and resid 497 through 499'
Processing sheet with id=AA1, first strand: chain 'B' and resid 79 through 83
removed outlier: 3.927A pdb=" N SER B 82 " --> pdb=" O GLU B 508 " (cutoff:3.500A)
removed outlier: 6.910A pdb=" N ASP B 300 " --> pdb=" O ILE B 246 " (cutoff:3.500A)
removed outlier: 5.715A pdb=" N ILE B 246 " --> pdb=" O ASP B 300 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'B' and resid 79 through 83
removed outlier: 3.927A pdb=" N SER B 82 " --> pdb=" O GLU B 508 " (cutoff:3.500A)
removed outlier: 7.862A pdb=" N VAL B 348 " --> pdb=" O GLN B 500 " (cutoff:3.500A)
removed outlier: 9.590A pdb=" N PHE B 502 " --> pdb=" O VAL B 348 " (cutoff:3.500A)
removed outlier: 11.720A pdb=" N LYS B 350 " --> pdb=" O PHE B 502 " (cutoff:3.500A)
removed outlier: 10.234A pdb=" N TYR B 504 " --> pdb=" O LYS B 350 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'B' and resid 90 through 91
removed outlier: 3.518A pdb=" N MET B 90 " --> pdb=" O SER B 286 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'B' and resid 262 through 266
Processing sheet with id=AA5, first strand: chain 'B' and resid 162 through 165
Processing sheet with id=AA6, first strand: chain 'B' and resid 361 through 362
Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 6
removed outlier: 3.549A pdb=" N UNK D 18 " --> pdb=" O UNK D 83 " (cutoff:3.500A)
removed outlier: 3.811A pdb=" N UNK D 78 " --> pdb=" O UNK D 73 " (cutoff:3.500A)
removed outlier: 3.917A pdb=" N UNK D 69 " --> pdb=" O UNK D 82 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'C' and resid 81 through 86
removed outlier: 9.430A pdb=" N ARG C 514 " --> pdb=" O MET C 357 " (cutoff:3.500A)
removed outlier: 6.397A pdb=" N LEU C 359 " --> pdb=" O ARG C 514 " (cutoff:3.500A)
removed outlier: 8.117A pdb=" N ILE C 516 " --> pdb=" O LEU C 359 " (cutoff:3.500A)
removed outlier: 6.693A pdb=" N GLU C 361 " --> pdb=" O ILE C 516 " (cutoff:3.500A)
removed outlier: 8.561A pdb=" N GLU C 518 " --> pdb=" O GLU C 361 " (cutoff:3.500A)
removed outlier: 8.489A pdb=" N PHE C 363 " --> pdb=" O GLU C 518 " (cutoff:3.500A)
removed outlier: 3.625A pdb=" N GLY C 356 " --> pdb=" O THR C 465 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'C' and resid 265 through 266
removed outlier: 6.700A pdb=" N ILE C 309 " --> pdb=" O VAL C 258 " (cutoff:3.500A)
removed outlier: 4.367A pdb=" N CYS C 260 " --> pdb=" O GLN C 307 " (cutoff:3.500A)
removed outlier: 6.703A pdb=" N GLN C 307 " --> pdb=" O CYS C 260 " (cutoff:3.500A)
removed outlier: 5.867A pdb=" N MET C 351 " --> pdb=" O LYS C 503 " (cutoff:3.500A)
removed outlier: 7.563A pdb=" N LEU C 505 " --> pdb=" O MET C 351 " (cutoff:3.500A)
removed outlier: 6.287A pdb=" N THR C 353 " --> pdb=" O LEU C 505 " (cutoff:3.500A)
removed outlier: 7.627A pdb=" N PHE C 507 " --> pdb=" O THR C 353 " (cutoff:3.500A)
removed outlier: 6.405A pdb=" N ILE C 355 " --> pdb=" O PHE C 507 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'C' and resid 92 through 93
Processing sheet with id=AB2, first strand: chain 'C' and resid 272 through 277
removed outlier: 6.752A pdb=" N ASN C 282 " --> pdb=" O ASN C 101 " (cutoff:3.500A)
removed outlier: 5.054A pdb=" N ASN C 101 " --> pdb=" O ASN C 282 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'C' and resid 172 through 173
removed outlier: 4.417A pdb=" N VAL C 202 " --> pdb=" O PHE C 219 " (cutoff:3.500A)
Processing sheet with id=AB4, first strand: chain 'E' and resid 5 through 6
309 hydrogen bonds defined for protein.
816 hydrogen bond angles defined for protein.
Restraints generated for nucleic acids:
0 hydrogen bonds
0 hydrogen bond angles
0 basepair planarities
0 basepair parallelities
0 stacking parallelities
Total time for adding SS restraints: 5.03
Time building geometry restraints manager: 4.66 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
0.84 - 1.03: 6422
1.03 - 1.23: 462
1.23 - 1.43: 2971
1.43 - 1.63: 4499
1.63 - 1.82: 88
Bond restraints: 14442
Sorted by residual:
bond pdb=" N THR C 80 "
pdb=" CA THR C 80 "
ideal model delta sigma weight residual
1.458 1.497 -0.039 1.90e-02 2.77e+03 4.19e+00
bond pdb=" N GLU B 78 "
pdb=" CA GLU B 78 "
ideal model delta sigma weight residual
1.458 1.496 -0.038 1.90e-02 2.77e+03 3.92e+00
bond pdb=" N UNK D 1 "
pdb=" CA UNK D 1 "
ideal model delta sigma weight residual
1.458 1.492 -0.034 1.90e-02 2.77e+03 3.19e+00
bond pdb=" N UNK E 1 "
pdb=" CA UNK E 1 "
ideal model delta sigma weight residual
1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00
bond pdb=" N THR C 80 "
pdb=" H THR C 80 "
ideal model delta sigma weight residual
0.860 0.892 -0.032 2.00e-02 2.50e+03 2.52e+00
... (remaining 14437 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 1.71: 24664
1.71 - 3.41: 721
3.41 - 5.12: 93
5.12 - 6.82: 20
6.82 - 8.53: 4
Bond angle restraints: 25502
Sorted by residual:
angle pdb=" N TRP C 431 "
pdb=" CA TRP C 431 "
pdb=" C TRP C 431 "
ideal model delta sigma weight residual
110.97 117.50 -6.53 1.09e+00 8.42e-01 3.58e+01
angle pdb=" N ILE B 246 "
pdb=" CA ILE B 246 "
pdb=" C ILE B 246 "
ideal model delta sigma weight residual
106.21 110.67 -4.46 1.07e+00 8.73e-01 1.74e+01
angle pdb=" C1 BMA I 3 "
pdb=" O5 BMA I 3 "
pdb=" C5 BMA I 3 "
ideal model delta sigma weight residual
118.82 110.29 8.53 3.00e+00 1.11e-01 8.08e+00
angle pdb=" C1 NAG J 1 "
pdb=" O5 NAG J 1 "
pdb=" C5 NAG J 1 "
ideal model delta sigma weight residual
113.21 121.24 -8.03 3.00e+00 1.11e-01 7.16e+00
angle pdb=" C1 BMA A 3 "
pdb=" O5 BMA A 3 "
pdb=" C5 BMA A 3 "
ideal model delta sigma weight residual
118.82 111.22 7.60 3.00e+00 1.11e-01 6.41e+00
... (remaining 25497 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 21.13: 6820
21.13 - 42.27: 292
42.27 - 63.40: 119
63.40 - 84.54: 29
84.54 - 105.67: 16
Dihedral angle restraints: 7276
sinusoidal: 3712
harmonic: 3564
Sorted by residual:
dihedral pdb=" CB CYS C 260 "
pdb=" SG CYS C 260 "
pdb=" SG CYS C 267 "
pdb=" CB CYS C 267 "
ideal model delta sinusoidal sigma weight residual
-86.00 -168.07 82.07 1 1.00e+01 1.00e-02 8.28e+01
dihedral pdb=" CB CYS C 394 "
pdb=" SG CYS C 394 "
pdb=" SG CYS C 453 "
pdb=" CB CYS C 453 "
ideal model delta sinusoidal sigma weight residual
93.00 170.05 -77.05 1 1.00e+01 1.00e-02 7.45e+01
dihedral pdb=" CB CYS B 361 "
pdb=" SG CYS B 361 "
pdb=" SG CYS B 448 "
pdb=" CB CYS B 448 "
ideal model delta sinusoidal sigma weight residual
93.00 167.90 -74.90 1 1.00e+01 1.00e-02 7.10e+01
... (remaining 7273 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.058: 1039
0.058 - 0.116: 195
0.116 - 0.174: 34
0.174 - 0.231: 6
0.231 - 0.289: 2
Chirality restraints: 1276
Sorted by residual:
chirality pdb=" C1 NAG H 2 "
pdb=" O4 NAG H 1 "
pdb=" C2 NAG H 2 "
pdb=" O5 NAG H 2 "
both_signs ideal model delta sigma weight residual
False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.53e+01
chirality pdb=" C1 NAG I 2 "
pdb=" O4 NAG I 1 "
pdb=" C2 NAG I 2 "
pdb=" O5 NAG I 2 "
both_signs ideal model delta sigma weight residual
False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.57e+01
chirality pdb=" C1 NAG A 2 "
pdb=" O4 NAG A 1 "
pdb=" C2 NAG A 2 "
pdb=" O5 NAG A 2 "
both_signs ideal model delta sigma weight residual
False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.28e+01
... (remaining 1273 not shown)
Planarity restraints: 2193
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C2 NAG A 1 " 0.045 2.00e-02 2.50e+03 3.76e-02 1.77e+01
pdb=" C7 NAG A 1 " -0.025 2.00e-02 2.50e+03
pdb=" C8 NAG A 1 " 0.038 2.00e-02 2.50e+03
pdb=" N2 NAG A 1 " -0.055 2.00e-02 2.50e+03
pdb=" O7 NAG A 1 " -0.003 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB ASN B 141 " 0.029 2.00e-02 2.50e+03 2.26e-02 7.69e+00
pdb=" CG ASN B 141 " -0.007 2.00e-02 2.50e+03
pdb=" OD1 ASN B 141 " -0.015 2.00e-02 2.50e+03
pdb=" ND2 ASN B 141 " -0.026 2.00e-02 2.50e+03
pdb="HD21 ASN B 141 " -0.014 2.00e-02 2.50e+03
pdb=" C1 NAG A 1 " 0.033 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C2 NAG H 1 " -0.030 2.00e-02 2.50e+03 2.46e-02 7.59e+00
pdb=" C7 NAG H 1 " 0.013 2.00e-02 2.50e+03
pdb=" C8 NAG H 1 " -0.024 2.00e-02 2.50e+03
pdb=" N2 NAG H 1 " 0.037 2.00e-02 2.50e+03
pdb=" O7 NAG H 1 " 0.003 2.00e-02 2.50e+03
... (remaining 2190 not shown)
Histogram of nonbonded interaction distances:
1.61 - 2.21: 694
2.21 - 2.80: 26824
2.80 - 3.40: 35628
3.40 - 4.00: 46261
4.00 - 4.60: 71322
Nonbonded interactions: 180729
Sorted by model distance:
nonbonded pdb=" OD1 ASN B 141 "
pdb=" HG SER B 143 "
model vdw
1.607 2.450
nonbonded pdb=" OE1 GLU C 341 "
pdb=" H GLU C 341 "
model vdw
1.648 2.450
nonbonded pdb=" OD2 ASP C 510 "
pdb="HD21 ASN C 512 "
model vdw
1.675 2.450
nonbonded pdb=" H ASP C 268 "
pdb="HD21 ASN C 271 "
model vdw
1.694 2.100
nonbonded pdb=" O VAL C 322 "
pdb=" HG SER C 323 "
model vdw
1.697 2.450
... (remaining 180724 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = chain 'H'
selection = chain 'I'
}
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 5.280
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.000
Construct map_model_manager: 0.250
Extract box with map and model: 0.500
Check model and map are aligned: 0.090
Set scattering table: 0.120
Process input model: 33.800
Find NCS groups from input model: 0.160
Set up NCS constraints: 0.090
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.010
Load rotamer database and sin/cos tables:3.040
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 43.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start: 0.0000
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.039 8020 Z= 0.349
Angle : 0.903 8.527 10906 Z= 0.467
Chirality : 0.050 0.289 1276
Planarity : 0.005 0.061 1396
Dihedral : 15.431 105.672 3016
Min Nonbonded Distance : 2.429
Molprobity Statistics.
All-atom Clashscore : 1.63
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.52 %
Favored : 96.48 %
Rotamer:
Outliers : 0.13 %
Allowed : 1.21 %
Favored : 98.66 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 7.89 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.60 (0.26), residues: 823
helix: -3.02 (0.25), residues: 221
sheet: -0.91 (0.35), residues: 186
loop : -1.26 (0.28), residues: 416
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.003 TRP C 229
HIS 0.010 0.003 HIS C 276
PHE 0.033 0.003 PHE B 328
TYR 0.024 0.002 TYR B 335
ARG 0.005 0.001 ARG B 330
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 176 is missing expected H atoms. Skipping.
Residue LYS 179 is missing expected H atoms. Skipping.
Residue SER 185 is missing expected H atoms. Skipping.
Residue ILE 186 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Evaluate side-chains
61 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 1
poor density : 60
time to evaluate : 1.079
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 101 SER cc_start: 0.9329 (t) cc_final: 0.8618 (p)
REVERT: B 337 MET cc_start: 0.8046 (ttt) cc_final: 0.7522 (ttm)
REVERT: C 351 MET cc_start: 0.8879 (mtt) cc_final: 0.8530 (mtt)
outliers start: 1
outliers final: 1
residues processed: 61
average time/residue: 0.5430
time to fit residues: 42.4286
Evaluate side-chains
38 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 1
poor density : 37
time to evaluate : 1.065
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 394 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 85 optimal weight: 3.9990
chunk 76 optimal weight: 3.9990
chunk 42 optimal weight: 7.9990
chunk 26 optimal weight: 4.9990
chunk 51 optimal weight: 5.9990
chunk 40 optimal weight: 0.5980
chunk 79 optimal weight: 10.0000
chunk 30 optimal weight: 1.9990
chunk 48 optimal weight: 9.9990
chunk 58 optimal weight: 3.9990
chunk 91 optimal weight: 2.9990
overall best weight: 2.7188
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.081179 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.061076 restraints weight = 79213.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.064038 restraints weight = 34657.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.066032 restraints weight = 21672.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start: 0.1686
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.051 8020 Z= 0.378
Angle : 0.744 7.811 10906 Z= 0.379
Chirality : 0.045 0.200 1276
Planarity : 0.004 0.042 1396
Dihedral : 10.140 56.654 1418
Min Nonbonded Distance : 2.364
Molprobity Statistics.
All-atom Clashscore : 4.97
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.43 %
Favored : 97.57 %
Rotamer:
Outliers : 0.40 %
Allowed : 4.44 %
Favored : 95.16 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 7.89 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.63 (0.28), residues: 823
helix: -1.19 (0.32), residues: 215
sheet: -1.15 (0.35), residues: 189
loop : -0.86 (0.30), residues: 419
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.002 TRP C 229
HIS 0.009 0.002 HIS C 276
PHE 0.026 0.002 PHE B 328
TYR 0.016 0.002 TYR C 129
ARG 0.004 0.001 ARG C 490
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 176 is missing expected H atoms. Skipping.
Residue LYS 179 is missing expected H atoms. Skipping.
Residue SER 185 is missing expected H atoms. Skipping.
Residue ILE 186 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Evaluate side-chains
42 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 3
poor density : 39
time to evaluate : 1.033
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 101 SER cc_start: 0.9301 (t) cc_final: 0.8605 (p)
REVERT: B 119 MET cc_start: 0.9128 (tpt) cc_final: 0.8919 (tpp)
REVERT: B 238 MET cc_start: 0.8850 (mtt) cc_final: 0.8493 (mtm)
REVERT: B 337 MET cc_start: 0.8110 (ttt) cc_final: 0.7546 (ttm)
REVERT: C 351 MET cc_start: 0.8865 (mtt) cc_final: 0.8508 (mtt)
outliers start: 3
outliers final: 2
residues processed: 40
average time/residue: 0.3641
time to fit residues: 21.4066
Evaluate side-chains
38 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 2
poor density : 36
time to evaluate : 1.088
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 394 CYS
Chi-restraints excluded: chain C residue 403 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 66 optimal weight: 0.7980
chunk 17 optimal weight: 1.9990
chunk 32 optimal weight: 2.9990
chunk 60 optimal weight: 4.9990
chunk 77 optimal weight: 0.9980
chunk 24 optimal weight: 1.9990
chunk 8 optimal weight: 1.9990
chunk 40 optimal weight: 1.9990
chunk 52 optimal weight: 7.9990
chunk 43 optimal weight: 10.0000
chunk 28 optimal weight: 0.8980
overall best weight: 1.3384
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.082182 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.062076 restraints weight = 78638.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.065098 restraints weight = 33758.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.067144 restraints weight = 20890.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start: 0.2099
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.024 8020 Z= 0.196
Angle : 0.592 6.141 10906 Z= 0.302
Chirality : 0.040 0.155 1276
Planarity : 0.004 0.042 1396
Dihedral : 7.458 46.868 1418
Min Nonbonded Distance : 2.417
Molprobity Statistics.
All-atom Clashscore : 3.27
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.67 %
Favored : 97.33 %
Rotamer:
Outliers : 0.40 %
Allowed : 4.84 %
Favored : 94.76 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 7.89 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.86 (0.29), residues: 823
helix: 0.10 (0.36), residues: 221
sheet: -1.05 (0.36), residues: 194
loop : -0.58 (0.31), residues: 408
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP C 229
HIS 0.005 0.001 HIS B 321
PHE 0.020 0.001 PHE B 328
TYR 0.013 0.001 TYR B 358
ARG 0.004 0.000 ARG C 172
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 176 is missing expected H atoms. Skipping.
Residue LYS 179 is missing expected H atoms. Skipping.
Residue SER 185 is missing expected H atoms. Skipping.
Residue ILE 186 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Evaluate side-chains
41 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 3
poor density : 38
time to evaluate : 1.079
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 101 SER cc_start: 0.9262 (t) cc_final: 0.8605 (p)
REVERT: B 119 MET cc_start: 0.9123 (tpt) cc_final: 0.8907 (tpp)
REVERT: B 337 MET cc_start: 0.8068 (ttt) cc_final: 0.7726 (ttm)
REVERT: C 351 MET cc_start: 0.8848 (mtt) cc_final: 0.8626 (mtt)
outliers start: 3
outliers final: 2
residues processed: 40
average time/residue: 0.3725
time to fit residues: 21.9975
Evaluate side-chains
38 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 2
poor density : 36
time to evaluate : 1.006
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 239 SER
Chi-restraints excluded: chain C residue 394 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 71 optimal weight: 2.9990
chunk 54 optimal weight: 4.9990
chunk 97 optimal weight: 7.9990
chunk 20 optimal weight: 2.9990
chunk 75 optimal weight: 0.7980
chunk 21 optimal weight: 1.9990
chunk 70 optimal weight: 0.6980
chunk 12 optimal weight: 3.9990
chunk 38 optimal weight: 4.9990
chunk 8 optimal weight: 2.9990
chunk 49 optimal weight: 7.9990
overall best weight: 1.8986
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.081494 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.061557 restraints weight = 79135.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.064537 restraints weight = 34563.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.066552 restraints weight = 21577.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start: 0.2480
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.032 8020 Z= 0.282
Angle : 0.591 5.121 10906 Z= 0.303
Chirality : 0.039 0.155 1276
Planarity : 0.004 0.047 1396
Dihedral : 6.707 46.965 1418
Min Nonbonded Distance : 2.458
Molprobity Statistics.
All-atom Clashscore : 4.49
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.28 %
Favored : 96.72 %
Rotamer:
Outliers : 0.40 %
Allowed : 5.91 %
Favored : 93.68 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 7.89 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.75 (0.30), residues: 823
helix: 0.43 (0.36), residues: 221
sheet: -1.11 (0.35), residues: 204
loop : -0.57 (0.32), residues: 398
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.002 TRP C 229
HIS 0.007 0.001 HIS C 276
PHE 0.022 0.001 PHE B 328
TYR 0.014 0.002 TYR C 129
ARG 0.002 0.000 ARG B 479
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 176 is missing expected H atoms. Skipping.
Residue LYS 179 is missing expected H atoms. Skipping.
Residue SER 185 is missing expected H atoms. Skipping.
Residue ILE 186 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Evaluate side-chains
41 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 3
poor density : 38
time to evaluate : 1.038
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 101 SER cc_start: 0.9259 (t) cc_final: 0.8550 (p)
REVERT: B 238 MET cc_start: 0.8832 (mtt) cc_final: 0.8464 (mtm)
REVERT: B 240 TYR cc_start: 0.8582 (m-80) cc_final: 0.8369 (m-80)
REVERT: B 337 MET cc_start: 0.8065 (ttt) cc_final: 0.7750 (ttm)
REVERT: C 299 MET cc_start: 0.8435 (mmm) cc_final: 0.8165 (mmm)
outliers start: 3
outliers final: 2
residues processed: 40
average time/residue: 0.4156
time to fit residues: 23.4355
Evaluate side-chains
39 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 2
poor density : 37
time to evaluate : 1.178
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 239 SER
Chi-restraints excluded: chain C residue 394 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 66 optimal weight: 1.9990
chunk 90 optimal weight: 2.9990
chunk 35 optimal weight: 4.9990
chunk 46 optimal weight: 7.9990
chunk 44 optimal weight: 8.9990
chunk 82 optimal weight: 1.9990
chunk 74 optimal weight: 3.9990
chunk 19 optimal weight: 2.9990
chunk 52 optimal weight: 8.9990
chunk 68 optimal weight: 0.6980
chunk 85 optimal weight: 0.9990
overall best weight: 1.7388
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.081644 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.061523 restraints weight = 80777.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.064546 restraints weight = 34649.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.066600 restraints weight = 21484.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start: 0.2684
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.046 8020 Z= 0.245
Angle : 0.563 5.604 10906 Z= 0.290
Chirality : 0.039 0.150 1276
Planarity : 0.004 0.085 1396
Dihedral : 6.494 49.667 1418
Min Nonbonded Distance : 2.468
Molprobity Statistics.
All-atom Clashscore : 4.77
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.79 %
Favored : 97.21 %
Rotamer:
Outliers : 0.40 %
Allowed : 6.05 %
Favored : 93.55 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 7.89 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.65 (0.30), residues: 823
helix: 0.57 (0.36), residues: 221
sheet: -1.14 (0.34), residues: 212
loop : -0.46 (0.33), residues: 390
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP C 229
HIS 0.006 0.001 HIS C 276
PHE 0.018 0.001 PHE B 328
TYR 0.012 0.001 TYR C 129
ARG 0.011 0.000 ARG B 388
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 176 is missing expected H atoms. Skipping.
Residue LYS 179 is missing expected H atoms. Skipping.
Residue SER 185 is missing expected H atoms. Skipping.
Residue ILE 186 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Evaluate side-chains
41 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 3
poor density : 38
time to evaluate : 1.133
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 101 SER cc_start: 0.9244 (t) cc_final: 0.8551 (p)
REVERT: B 238 MET cc_start: 0.8877 (mtt) cc_final: 0.8492 (mtm)
REVERT: C 299 MET cc_start: 0.8454 (mmm) cc_final: 0.8174 (mmm)
outliers start: 3
outliers final: 3
residues processed: 40
average time/residue: 0.3763
time to fit residues: 22.5300
Evaluate side-chains
39 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 3
poor density : 36
time to evaluate : 1.127
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 239 SER
Chi-restraints excluded: chain B residue 256 CYS
Chi-restraints excluded: chain C residue 394 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 48 optimal weight: 10.0000
chunk 44 optimal weight: 8.9990
chunk 68 optimal weight: 0.6980
chunk 86 optimal weight: 0.9990
chunk 65 optimal weight: 1.9990
chunk 11 optimal weight: 4.9990
chunk 78 optimal weight: 0.8980
chunk 49 optimal weight: 0.6980
chunk 31 optimal weight: 0.9990
chunk 13 optimal weight: 2.9990
chunk 0 optimal weight: 40.0000
overall best weight: 0.8584
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
C 512 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.082185 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.062288 restraints weight = 80308.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.065351 restraints weight = 33870.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.067413 restraints weight = 20813.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start: 0.2886
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.033 8020 Z= 0.158
Angle : 0.504 5.347 10906 Z= 0.260
Chirality : 0.038 0.154 1276
Planarity : 0.004 0.052 1396
Dihedral : 6.005 52.048 1418
Min Nonbonded Distance : 2.452
Molprobity Statistics.
All-atom Clashscore : 4.29
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.67 %
Favored : 97.33 %
Rotamer:
Outliers : 0.67 %
Allowed : 6.05 %
Favored : 93.28 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 7.89 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.34 (0.30), residues: 823
helix: 0.93 (0.36), residues: 215
sheet: -1.00 (0.34), residues: 212
loop : -0.29 (0.33), residues: 396
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP C 229
HIS 0.004 0.001 HIS B 321
PHE 0.015 0.001 PHE B 328
TYR 0.010 0.001 TYR C 217
ARG 0.008 0.000 ARG B 388
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 176 is missing expected H atoms. Skipping.
Residue LYS 179 is missing expected H atoms. Skipping.
Residue SER 185 is missing expected H atoms. Skipping.
Residue ILE 186 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Evaluate side-chains
45 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 5
poor density : 40
time to evaluate : 1.124
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 101 SER cc_start: 0.9203 (t) cc_final: 0.8410 (p)
REVERT: B 240 TYR cc_start: 0.8389 (m-80) cc_final: 0.8158 (m-80)
REVERT: B 337 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7992 (ttm)
REVERT: C 299 MET cc_start: 0.8484 (mmm) cc_final: 0.8208 (mmm)
REVERT: C 351 MET cc_start: 0.8931 (mtt) cc_final: 0.8724 (mtt)
outliers start: 5
outliers final: 2
residues processed: 43
average time/residue: 0.3665
time to fit residues: 22.9833
Evaluate side-chains
39 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 3
poor density : 36
time to evaluate : 1.170
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 239 SER
Chi-restraints excluded: chain B residue 337 MET
Chi-restraints excluded: chain C residue 394 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 22 optimal weight: 0.3980
chunk 73 optimal weight: 2.9990
chunk 93 optimal weight: 6.9990
chunk 26 optimal weight: 6.9990
chunk 52 optimal weight: 8.9990
chunk 57 optimal weight: 2.9990
chunk 75 optimal weight: 3.9990
chunk 91 optimal weight: 5.9990
chunk 94 optimal weight: 8.9990
chunk 31 optimal weight: 0.9980
chunk 69 optimal weight: 5.9990
overall best weight: 2.2786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 139 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.081270 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.061171 restraints weight = 81096.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.064150 restraints weight = 35297.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.066153 restraints weight = 22102.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start: 0.3116
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.036 8020 Z= 0.316
Angle : 0.574 5.822 10906 Z= 0.294
Chirality : 0.039 0.166 1276
Planarity : 0.004 0.051 1396
Dihedral : 6.248 55.876 1418
Min Nonbonded Distance : 2.418
Molprobity Statistics.
All-atom Clashscore : 5.79
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.52 %
Favored : 96.48 %
Rotamer:
Outliers : 0.54 %
Allowed : 6.59 %
Favored : 92.88 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 7.89 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.47 (0.30), residues: 823
helix: 0.82 (0.36), residues: 221
sheet: -1.14 (0.34), residues: 215
loop : -0.33 (0.34), residues: 387
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.002 TRP C 229
HIS 0.007 0.001 HIS C 276
PHE 0.021 0.001 PHE B 328
TYR 0.013 0.001 TYR C 129
ARG 0.007 0.001 ARG B 388
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 176 is missing expected H atoms. Skipping.
Residue LYS 179 is missing expected H atoms. Skipping.
Residue SER 185 is missing expected H atoms. Skipping.
Residue ILE 186 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Evaluate side-chains
40 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 36
time to evaluate : 1.140
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 101 SER cc_start: 0.9244 (t) cc_final: 0.8550 (p)
outliers start: 4
outliers final: 3
residues processed: 38
average time/residue: 0.2998
time to fit residues: 18.0022
Evaluate side-chains
38 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 3
poor density : 35
time to evaluate : 1.118
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 239 SER
Chi-restraints excluded: chain B residue 256 CYS
Chi-restraints excluded: chain C residue 394 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 18 optimal weight: 1.9990
chunk 71 optimal weight: 4.9990
chunk 82 optimal weight: 1.9990
chunk 48 optimal weight: 9.9990
chunk 95 optimal weight: 10.0000
chunk 12 optimal weight: 2.9990
chunk 25 optimal weight: 3.9990
chunk 94 optimal weight: 8.9990
chunk 43 optimal weight: 10.0000
chunk 36 optimal weight: 0.8980
chunk 29 optimal weight: 1.9990
overall best weight: 1.9788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.081305 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.061296 restraints weight = 81091.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.064282 restraints weight = 35569.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.066272 restraints weight = 22308.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start: 0.3245
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.030 8020 Z= 0.271
Angle : 0.547 6.494 10906 Z= 0.280
Chirality : 0.038 0.149 1276
Planarity : 0.004 0.049 1396
Dihedral : 6.329 59.322 1418
Min Nonbonded Distance : 2.410
Molprobity Statistics.
All-atom Clashscore : 5.65
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.28 %
Favored : 96.72 %
Rotamer:
Outliers : 0.54 %
Allowed : 6.72 %
Favored : 92.74 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 7.89 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.44 (0.31), residues: 823
helix: 0.88 (0.36), residues: 221
sheet: -1.22 (0.34), residues: 215
loop : -0.27 (0.35), residues: 387
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP C 229
HIS 0.006 0.001 HIS C 276
PHE 0.017 0.001 PHE B 328
TYR 0.012 0.001 TYR C 129
ARG 0.005 0.000 ARG B 388
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 176 is missing expected H atoms. Skipping.
Residue LYS 179 is missing expected H atoms. Skipping.
Residue SER 185 is missing expected H atoms. Skipping.
Residue ILE 186 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Evaluate side-chains
40 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 36
time to evaluate : 1.148
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 101 SER cc_start: 0.9233 (t) cc_final: 0.8540 (p)
outliers start: 4
outliers final: 3
residues processed: 38
average time/residue: 0.2963
time to fit residues: 17.8340
Evaluate side-chains
38 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 3
poor density : 35
time to evaluate : 1.051
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 239 SER
Chi-restraints excluded: chain B residue 256 CYS
Chi-restraints excluded: chain C residue 394 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 72 optimal weight: 4.9990
chunk 99 optimal weight: 9.9990
chunk 78 optimal weight: 2.9990
chunk 35 optimal weight: 0.9990
chunk 17 optimal weight: 1.9990
chunk 56 optimal weight: 2.9990
chunk 36 optimal weight: 2.9990
chunk 95 optimal weight: 10.0000
chunk 23 optimal weight: 1.9990
chunk 60 optimal weight: 2.9990
chunk 96 optimal weight: 10.0000
overall best weight: 2.1990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.080799 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.060757 restraints weight = 81877.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.063754 restraints weight = 35244.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.065736 restraints weight = 21943.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start: 0.3422
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.041 8020 Z= 0.315
Angle : 0.582 7.063 10906 Z= 0.296
Chirality : 0.039 0.152 1276
Planarity : 0.004 0.052 1396
Dihedral : 6.427 59.893 1418
Min Nonbonded Distance : 2.387
Molprobity Statistics.
All-atom Clashscore : 6.13
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.52 %
Favored : 96.48 %
Rotamer:
Outliers : 0.54 %
Allowed : 6.72 %
Favored : 92.74 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 7.89 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.58 (0.30), residues: 823
helix: 0.85 (0.36), residues: 221
sheet: -1.26 (0.33), residues: 217
loop : -0.44 (0.34), residues: 385
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP C 229
HIS 0.007 0.001 HIS B 321
PHE 0.019 0.001 PHE B 328
TYR 0.013 0.001 TYR C 129
ARG 0.006 0.001 ARG B 388
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 176 is missing expected H atoms. Skipping.
Residue LYS 179 is missing expected H atoms. Skipping.
Residue SER 185 is missing expected H atoms. Skipping.
Residue ILE 186 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Evaluate side-chains
41 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 37
time to evaluate : 1.156
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 101 SER cc_start: 0.9231 (t) cc_final: 0.8517 (p)
REVERT: B 238 MET cc_start: 0.8916 (mtt) cc_final: 0.8596 (mtm)
outliers start: 4
outliers final: 4
residues processed: 40
average time/residue: 0.3170
time to fit residues: 20.0317
Evaluate side-chains
38 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 34
time to evaluate : 1.184
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 239 SER
Chi-restraints excluded: chain B residue 256 CYS
Chi-restraints excluded: chain B residue 399 CYS
Chi-restraints excluded: chain C residue 394 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 66 optimal weight: 0.6980
chunk 99 optimal weight: 10.0000
chunk 34 optimal weight: 5.9990
chunk 12 optimal weight: 3.9990
chunk 62 optimal weight: 1.9990
chunk 83 optimal weight: 2.9990
chunk 30 optimal weight: 0.9980
chunk 64 optimal weight: 0.9980
chunk 85 optimal weight: 0.8980
chunk 29 optimal weight: 0.6980
chunk 96 optimal weight: 9.9990
overall best weight: 0.8580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.082179 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.062155 restraints weight = 81120.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.065188 restraints weight = 35260.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.067196 restraints weight = 21936.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start: 0.3536
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.035 8020 Z= 0.150
Angle : 0.503 7.074 10906 Z= 0.255
Chirality : 0.037 0.154 1276
Planarity : 0.003 0.043 1396
Dihedral : 6.062 57.692 1418
Min Nonbonded Distance : 2.417
Molprobity Statistics.
All-atom Clashscore : 5.31
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.31 %
Favored : 97.69 %
Rotamer:
Outliers : 0.67 %
Allowed : 6.32 %
Favored : 93.01 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 7.89 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.22 (0.31), residues: 823
helix: 1.33 (0.37), residues: 209
sheet: -1.21 (0.33), residues: 219
loop : -0.17 (0.34), residues: 395
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP C 229
HIS 0.005 0.001 HIS B 321
PHE 0.011 0.001 PHE B 328
TYR 0.010 0.001 TYR B 273
ARG 0.005 0.000 ARG B 388
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1646 Ramachandran restraints generated.
823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR 176 is missing expected H atoms. Skipping.
Residue LYS 179 is missing expected H atoms. Skipping.
Residue SER 185 is missing expected H atoms. Skipping.
Residue ILE 186 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Evaluate side-chains
42 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 5
poor density : 37
time to evaluate : 1.064
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 101 SER cc_start: 0.9210 (t) cc_final: 0.8497 (p)
outliers start: 5
outliers final: 4
residues processed: 41
average time/residue: 0.2800
time to fit residues: 18.1550
Evaluate side-chains
40 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 36
time to evaluate : 1.041
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 256 CYS
Chi-restraints excluded: chain B residue 337 MET
Chi-restraints excluded: chain B residue 399 CYS
Chi-restraints excluded: chain C residue 394 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 14 optimal weight: 2.9990
chunk 76 optimal weight: 4.9990
chunk 94 optimal weight: 9.9990
chunk 33 optimal weight: 3.9990
chunk 56 optimal weight: 2.9990
chunk 12 optimal weight: 3.9990
chunk 60 optimal weight: 3.9990
chunk 21 optimal weight: 0.9990
chunk 75 optimal weight: 0.8980
chunk 95 optimal weight: 9.9990
chunk 68 optimal weight: 3.9990
overall best weight: 2.3788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.080997 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.061000 restraints weight = 81683.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.063973 restraints weight = 35529.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.065938 restraints weight = 22212.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start: 0.3610
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.039 8020 Z= 0.313
Angle : 0.570 7.202 10906 Z= 0.290
Chirality : 0.038 0.148 1276
Planarity : 0.004 0.048 1396
Dihedral : 6.260 59.942 1418
Min Nonbonded Distance : 2.395
Molprobity Statistics.
All-atom Clashscore : 6.60
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.65 %
Favored : 96.35 %
Rotamer:
Outliers : 0.54 %
Allowed : 6.72 %
Favored : 92.74 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 7.89 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.49 (0.31), residues: 823
helix: 1.02 (0.36), residues: 221
sheet: -1.31 (0.34), residues: 219
loop : -0.36 (0.34), residues: 383
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.002 TRP C 229
HIS 0.007 0.001 HIS C 276
PHE 0.021 0.001 PHE B 328
TYR 0.014 0.001 TYR B 326
ARG 0.005 0.000 ARG B 388
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 4186.40 seconds
wall clock time: 75 minutes 14.74 seconds (4514.74 seconds total)