Starting phenix.real_space_refine (version: dev)
on Thu Jul 7 02:02:08 2022 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsu_12577/07_2022/7nsu_12577.pdb
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsu_12577/07_2022/7nsu_12577.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=4.7
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsu_12577/07_2022/7nsu_12577.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsu_12577/07_2022/7nsu_12577.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsu_12577/07_2022/7nsu_12577.pdb"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsu_12577/07_2022/7nsu_12577.pdb"
}
resolution = 4.7
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
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
-------------------------------------------------------------------------------
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= 0.002 sd= 0.033
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
Convert atoms to be neutral
Process input model
Symmetric amino acids flipped
None
Time to flip residues: 0.05s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-4648/modules/chem_data/mon_lib"
Total number of atoms: 36070
Number of models: 1
Model: ""
Number of chains: 6
Chain: "A"
Number of atoms: 5071
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 340, 5071
Classifications: {'peptide': 340}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 4, 'TRANS': 335}
Chain: "B"
Number of atoms: 5071
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 340, 5071
Classifications: {'peptide': 340}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 4, 'TRANS': 335}
Chain: "C"
Number of atoms: 5070
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 340, 5070
Classifications: {'peptide': 340}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 4, 'TRANS': 335}
Chain: "D"
Number of atoms: 6003
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 420, 6003
Classifications: {'peptide': 420}
Link IDs: {'PTRANS': 24, 'TRANS': 395}
Chain breaks: 2
Unresolved non-hydrogen bonds: 28
Unresolved non-hydrogen angles: 36
Unresolved non-hydrogen dihedrals: 20
Unresolved non-hydrogen chiralities: 5
Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1}
Unresolved non-hydrogen planarities: 11
Chain: "E"
Number of atoms: 6000
Number of conformers: 2
Conformer: "A"
Number of residues, atoms: 394, 5856
Classifications: {'peptide': 394}
Link IDs: {'PTRANS': 26, 'TRANS': 367}
Chain breaks: 1
Conformer: "B"
Number of residues, atoms: 394, 5856
Classifications: {'peptide': 394}
Link IDs: {'PTRANS': 26, 'TRANS': 367}
Chain breaks: 1
bond proxies already assigned to first conformer: 5772
Chain: "F"
Number of atoms: 8855
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 576, 8855
Classifications: {'peptide': 576}
Modifications used: {'COO': 1}
Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 557}
Chain breaks: 1
Time building chain proxies: 18.28, per 1000 atoms: 0.51
Number of scatterers: 36070
At special positions: 0
Unit cell: (189.507, 100.512, 145.533, 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 27 16.00
O 3707 8.00
N 3196 7.00
C 11613 6.00
H 17527 1.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=1, symmetry=0
Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS E 201 " distance=2.05
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.50
Amino acid : False - 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
Time building additional restraints: 31.09
Conformation dependent library (CDL) restraints added in 3.9 seconds
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 4266
Finding SS restraints...
Secondary structure from input PDB file:
34 helices and 21 sheets defined
14.7% alpha, 42.7% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.06
Creating SS restraints...
Processing helix chain 'A' and resid 103 through 110
removed outlier: 3.533A pdb=" N ASP A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A)
removed outlier: 3.668A pdb=" N ALA A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A)
Processing helix chain 'A' and resid 142 through 147
Processing helix chain 'A' and resid 197 through 202
Processing helix chain 'B' and resid 103 through 110
removed outlier: 3.523A pdb=" N ASP B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A)
removed outlier: 3.646A pdb=" N ALA B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A)
Processing helix chain 'B' and resid 142 through 147
Processing helix chain 'B' and resid 165 through 169
Processing helix chain 'B' and resid 197 through 203
Processing helix chain 'C' and resid 103 through 110
removed outlier: 3.630A pdb=" N ASP C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A)
removed outlier: 3.693A pdb=" N ALA C 108 " --> pdb=" O VAL C 104 " (cutoff:3.500A)
Processing helix chain 'C' and resid 142 through 147
Processing helix chain 'C' and resid 197 through 203
Processing helix chain 'D' and resid 113 through 125
removed outlier: 3.607A pdb=" N LYS D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A)
Processing helix chain 'D' and resid 141 through 149
removed outlier: 3.916A pdb=" N LYS D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A)
removed outlier: 3.871A pdb=" N ASP D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A)
Processing helix chain 'D' and resid 162 through 166
Processing helix chain 'D' and resid 276 through 280
removed outlier: 3.853A pdb=" N GLY D 280 " --> pdb=" O LYS D 277 " (cutoff:3.500A)
Processing helix chain 'D' and resid 293 through 313
removed outlier: 3.922A pdb=" N ALA D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A)
Processing helix chain 'D' and resid 317 through 377
removed outlier: 3.813A pdb=" N GLU D 321 " --> pdb=" O VAL D 317 " (cutoff:3.500A)
removed outlier: 3.578A pdb=" N ASN D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A)
removed outlier: 4.072A pdb=" N TYR D 324 " --> pdb=" O ALA D 320 " (cutoff:3.500A)
removed outlier: 3.507A pdb=" N GLN D 350 " --> pdb=" O ALA D 346 " (cutoff:3.500A)
Processing helix chain 'D' and resid 378 through 382
removed outlier: 4.263A pdb=" N HIS D 381 " --> pdb=" O ARG D 378 " (cutoff:3.500A)
Processing helix chain 'D' and resid 386 through 446
removed outlier: 3.695A pdb=" N MET D 390 " --> pdb=" O GLY D 386 " (cutoff:3.500A)
removed outlier: 4.098A pdb=" N GLN D 392 " --> pdb=" O HIS D 388 " (cutoff:3.500A)
removed outlier: 3.580A pdb=" N SER D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A)
Processing helix chain 'E' and resid 53 through 65
Processing helix chain 'E' and resid 72 through 76
Processing helix chain 'E' and resid 87 through 93
removed outlier: 3.739A pdb=" N TRP E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A)
Processing helix chain 'E' and resid 137 through 139
No H-bonds generated for 'chain 'E' and resid 137 through 139'
Processing helix chain 'E' and resid 140 through 158
Processing helix chain 'E' and resid 394 through 399
Processing helix chain 'F' and resid 20 through 22
No H-bonds generated for 'chain 'F' and resid 20 through 22'
Processing helix chain 'F' and resid 31 through 38
Processing helix chain 'F' and resid 41 through 47
Processing helix chain 'F' and resid 70 through 71
No H-bonds generated for 'chain 'F' and resid 70 through 71'
Processing helix chain 'F' and resid 72 through 76
removed outlier: 3.654A pdb=" N VAL F 76 " --> pdb=" O ALA F 73 " (cutoff:3.500A)
Processing helix chain 'F' and resid 87 through 92
removed outlier: 4.625A pdb=" N SER F 91 " --> pdb=" O LEU F 87 " (cutoff:3.500A)
Processing helix chain 'F' and resid 100 through 104
removed outlier: 3.692A pdb=" N LEU F 103 " --> pdb=" O PRO F 100 " (cutoff:3.500A)
Processing helix chain 'F' and resid 114 through 119
Processing helix chain 'F' and resid 325 through 329
removed outlier: 3.519A pdb=" N VAL F 329 " --> pdb=" O THR F 326 " (cutoff:3.500A)
Processing helix chain 'F' and resid 397 through 403
Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6
WARNING: can't find start of bonding for strands!
previous: chain 'A' and resid 2 through 6
current: chain 'A' and resid 55 through 66
removed outlier: 6.444A pdb=" N ASN A 64 " --> pdb=" O THR A 81 " (cutoff:3.500A)
removed outlier: 5.232A pdb=" N THR A 81 " --> pdb=" O ASN A 64 " (cutoff:3.500A)
removed outlier: 12.494A pdb=" N ARG A 82 " --> pdb=" O TYR A 102 " (cutoff:3.500A)
removed outlier: 6.621A pdb=" N TYR A 102 " --> pdb=" O ARG A 82 " (cutoff:3.500A)
removed outlier: 6.848A pdb=" N ASN A 101 " --> pdb=" O GLY A 134 " (cutoff:3.500A)
removed outlier: 5.087A pdb=" N GLY A 134 " --> pdb=" O ASN A 101 " (cutoff:3.500A)
removed outlier: 7.251A pdb=" N ILE A 273 " --> pdb=" O VAL A 297 " (cutoff:3.500A)
removed outlier: 7.053A pdb=" N VAL A 297 " --> pdb=" O ILE A 273 " (cutoff:3.500A)
removed outlier: 6.727A pdb=" N TYR A 275 " --> pdb=" O PHE A 295 " (cutoff:3.500A)
removed outlier: 7.116A pdb=" N PHE A 295 " --> pdb=" O TYR A 275 " (cutoff:3.500A)
removed outlier: 7.032A pdb=" N LYS A 277 " --> pdb=" O ASN A 293 " (cutoff:3.500A)
removed outlier: 6.629A pdb=" N ASN A 293 " --> pdb=" O LYS A 277 " (cutoff:3.500A)
removed outlier: 7.607A pdb=" N LYS A 279 " --> pdb=" O LEU A 291 " (cutoff:3.500A)
removed outlier: 6.390A pdb=" N LEU A 291 " --> pdb=" O LYS A 279 " (cutoff:3.500A)
removed outlier: 5.090A pdb=" N LYS A 281 " --> pdb=" O VAL A 289 " (cutoff:3.500A)
removed outlier: 6.927A pdb=" N VAL A 289 " --> pdb=" O LYS A 281 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 242
Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 6
WARNING: can't find start of bonding for strands!
previous: chain 'B' and resid 2 through 6
current: chain 'B' and resid 55 through 66
removed outlier: 6.440A pdb=" N ASN B 64 " --> pdb=" O THR B 81 " (cutoff:3.500A)
removed outlier: 5.260A pdb=" N THR B 81 " --> pdb=" O ASN B 64 " (cutoff:3.500A)
removed outlier: 12.549A pdb=" N ARG B 82 " --> pdb=" O TYR B 102 " (cutoff:3.500A)
removed outlier: 6.602A pdb=" N TYR B 102 " --> pdb=" O ARG B 82 " (cutoff:3.500A)
removed outlier: 6.898A pdb=" N ASN B 101 " --> pdb=" O GLY B 134 " (cutoff:3.500A)
removed outlier: 5.162A pdb=" N GLY B 134 " --> pdb=" O ASN B 101 " (cutoff:3.500A)
removed outlier: 3.697A pdb=" N VAL B 292 " --> pdb=" O SER B 278 " (cutoff:3.500A)
removed outlier: 6.528A pdb=" N ALA B 280 " --> pdb=" O ASP B 290 " (cutoff:3.500A)
removed outlier: 5.360A pdb=" N ASP B 290 " --> pdb=" O ALA B 280 " (cutoff:3.500A)
removed outlier: 7.239A pdb=" N ASP B 282 " --> pdb=" O ASP B 288 " (cutoff:3.500A)
removed outlier: 7.101A pdb=" N ASP B 288 " --> pdb=" O ASP B 282 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 242
Processing sheet with id=AA5, first strand: chain 'C' and resid 2 through 6
WARNING: can't find start of bonding for strands!
previous: chain 'C' and resid 2 through 6
current: chain 'C' and resid 55 through 66
removed outlier: 6.538A pdb=" N ASN C 64 " --> pdb=" O THR C 81 " (cutoff:3.500A)
removed outlier: 5.306A pdb=" N THR C 81 " --> pdb=" O ASN C 64 " (cutoff:3.500A)
removed outlier: 12.536A pdb=" N ARG C 82 " --> pdb=" O TYR C 102 " (cutoff:3.500A)
removed outlier: 6.660A pdb=" N TYR C 102 " --> pdb=" O ARG C 82 " (cutoff:3.500A)
removed outlier: 6.925A pdb=" N ASN C 101 " --> pdb=" O GLY C 134 " (cutoff:3.500A)
removed outlier: 5.256A pdb=" N GLY C 134 " --> pdb=" O ASN C 101 " (cutoff:3.500A)
removed outlier: 3.569A pdb=" N VAL C 292 " --> pdb=" O SER C 278 " (cutoff:3.500A)
removed outlier: 6.450A pdb=" N ALA C 280 " --> pdb=" O ASP C 290 " (cutoff:3.500A)
removed outlier: 5.275A pdb=" N ASP C 290 " --> pdb=" O ALA C 280 " (cutoff:3.500A)
removed outlier: 7.055A pdb=" N ASP C 282 " --> pdb=" O ASP C 288 " (cutoff:3.500A)
removed outlier: 6.933A pdb=" N ASP C 288 " --> pdb=" O ASP C 282 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'C' and resid 239 through 242
Processing sheet with id=AA7, first strand: chain 'D' and resid 94 through 96
removed outlier: 19.821A pdb=" N THR D 268 " --> pdb=" O GLY D 202 " (cutoff:3.500A)
removed outlier: 13.991A pdb=" N ASP D 270 " --> pdb=" O PRO D 204 " (cutoff:3.500A)
removed outlier: 9.341A pdb=" N SER D 206 " --> pdb=" O ASP D 270 " (cutoff:3.500A)
removed outlier: 8.329A pdb=" N VAL D 272 " --> pdb=" O SER D 206 " (cutoff:3.500A)
removed outlier: 7.583A pdb=" N ARG D 274 " --> pdb=" O PRO D 208 " (cutoff:3.500A)
removed outlier: 6.425A pdb=" N VAL D 210 " --> pdb=" O ARG D 274 " (cutoff:3.500A)
removed outlier: 4.125A pdb=" N GLY D 202 " --> pdb=" O ASN D 183 " (cutoff:3.500A)
removed outlier: 9.572A pdb=" N ASN D 183 " --> pdb=" O GLY D 202 " (cutoff:3.500A)
removed outlier: 9.097A pdb=" N ASN D 181 " --> pdb=" O PRO D 204 " (cutoff:3.500A)
removed outlier: 7.147A pdb=" N SER D 206 " --> pdb=" O THR D 179 " (cutoff:3.500A)
removed outlier: 7.400A pdb=" N THR D 179 " --> pdb=" O SER D 206 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'D' and resid 94 through 96
removed outlier: 19.821A pdb=" N THR D 268 " --> pdb=" O GLY D 202 " (cutoff:3.500A)
removed outlier: 13.991A pdb=" N ASP D 270 " --> pdb=" O PRO D 204 " (cutoff:3.500A)
removed outlier: 9.341A pdb=" N SER D 206 " --> pdb=" O ASP D 270 " (cutoff:3.500A)
removed outlier: 8.329A pdb=" N VAL D 272 " --> pdb=" O SER D 206 " (cutoff:3.500A)
removed outlier: 7.583A pdb=" N ARG D 274 " --> pdb=" O PRO D 208 " (cutoff:3.500A)
removed outlier: 6.425A pdb=" N VAL D 210 " --> pdb=" O ARG D 274 " (cutoff:3.500A)
removed outlier: 7.549A pdb=" N GLN D 195 " --> pdb=" O SER D 139 " (cutoff:3.500A)
removed outlier: 5.180A pdb=" N SER D 139 " --> pdb=" O GLN D 195 " (cutoff:3.500A)
removed outlier: 6.876A pdb=" N ILE D 197 " --> pdb=" O LEU D 137 " (cutoff:3.500A)
removed outlier: 3.642A pdb=" N SER D 201 " --> pdb=" O PHE D 133 " (cutoff:3.500A)
removed outlier: 4.326A pdb=" N PHE D 133 " --> pdb=" O SER D 201 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'D' and resid 103 through 104
removed outlier: 6.458A pdb=" N LEU D 103 " --> pdb=" O ASN D 232 " (cutoff:3.500A)
removed outlier: 8.125A pdb=" N SER D 234 " --> pdb=" O LEU D 103 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'E' and resid 68 through 70
removed outlier: 9.130A pdb=" N VAL E 100 " --> pdb=" O PRO E 36 " (cutoff:3.500A)
removed outlier: 6.892A pdb=" N GLY E 38 " --> pdb=" O VAL E 100 " (cutoff:3.500A)
removed outlier: 8.801A pdb=" N GLY E 102 " --> pdb=" O GLY E 38 " (cutoff:3.500A)
removed outlier: 3.702A pdb=" N ALA E 130 " --> pdb=" O LEU E 118 " (cutoff:3.500A)
removed outlier: 6.379A pdb=" N ASP E 120 " --> pdb=" O VAL E 128 " (cutoff:3.500A)
removed outlier: 6.210A pdb=" N VAL E 128 " --> pdb=" O ASP E 120 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'E' and resid 193 through 198
removed outlier: 5.195A pdb=" N VAL E 194 " --> pdb=" O VAL E 184 " (cutoff:3.500A)
removed outlier: 6.234A pdb=" N VAL E 184 " --> pdb=" O VAL E 194 " (cutoff:3.500A)
removed outlier: 6.956A pdb=" N ARG E 166 " --> pdb=" O TRP E 426 " (cutoff:3.500A)
removed outlier: 4.920A pdb=" N TRP E 426 " --> pdb=" O ARG E 166 " (cutoff:3.500A)
removed outlier: 6.382A pdb=" N ALA E 168 " --> pdb=" O PRO E 424 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'E' and resid 206 through 207
removed outlier: 3.546A pdb=" N ALA E 206 " --> pdb=" O ALA E 215 " (cutoff:3.500A)
removed outlier: 6.361A pdb=" N LEU E 226 " --> pdb=" O VAL E 239 " (cutoff:3.500A)
Processing sheet with id=AB4, first strand: chain 'E' and resid 246 through 251
removed outlier: 5.322A pdb=" N ALA E 248 " --> pdb=" O ALA E 261 " (cutoff:3.500A)
removed outlier: 4.101A pdb=" N ALA E 261 " --> pdb=" O ALA E 248 " (cutoff:3.500A)
Processing sheet with id=AB5, first strand: chain 'E' and resid 290 through 295
removed outlier: 5.548A pdb=" N GLU E 292 " --> pdb=" O THR E 305 " (cutoff:3.500A)
removed outlier: 4.296A pdb=" N THR E 305 " --> pdb=" O GLU E 292 " (cutoff:3.500A)
Processing sheet with id=AB6, first strand: chain 'E' and resid 333 through 339
removed outlier: 4.674A pdb=" N ALA E 337 " --> pdb=" O VAL E 347 " (cutoff:3.500A)
removed outlier: 7.015A pdb=" N VAL E 347 " --> pdb=" O ALA E 337 " (cutoff:3.500A)
removed outlier: 5.274A pdb=" N VAL E 339 " --> pdb=" O PHE E 345 " (cutoff:3.500A)
removed outlier: 7.368A pdb=" N PHE E 345 " --> pdb=" O VAL E 339 " (cutoff:3.500A)
removed outlier: 3.671A pdb=" N GLN E 355 " --> pdb=" O ASN E 352 " (cutoff:3.500A)
Processing sheet with id=AB7, first strand: chain 'E' and resid 378 through 382
removed outlier: 5.407A pdb=" N THR E 379 " --> pdb=" O SER E 392 " (cutoff:3.500A)
removed outlier: 4.257A pdb=" N SER E 392 " --> pdb=" O THR E 379 " (cutoff:3.500A)
Processing sheet with id=AB8, first strand: chain 'F' and resid 8 through 9
Processing sheet with id=AB9, first strand: chain 'F' and resid 26 through 30
Processing sheet with id=AC1, first strand: chain 'F' and resid 52 through 56
Processing sheet with id=AC2, first strand: chain 'F' and resid 137 through 145
removed outlier: 8.805A pdb=" N THR F 370 " --> pdb=" O TYR F 393 " (cutoff:3.500A)
removed outlier: 7.969A pdb=" N TYR F 393 " --> pdb=" O THR F 370 " (cutoff:3.500A)
removed outlier: 4.961A pdb=" N GLN F 372 " --> pdb=" O THR F 391 " (cutoff:3.500A)
removed outlier: 7.053A pdb=" N THR F 391 " --> pdb=" O GLN F 372 " (cutoff:3.500A)
removed outlier: 5.205A pdb=" N SER F 374 " --> pdb=" O TYR F 389 " (cutoff:3.500A)
removed outlier: 7.355A pdb=" N TYR F 389 " --> pdb=" O SER F 374 " (cutoff:3.500A)
removed outlier: 5.360A pdb=" N GLY F 376 " --> pdb=" O ALA F 387 " (cutoff:3.500A)
removed outlier: 7.558A pdb=" N ALA F 387 " --> pdb=" O GLY F 376 " (cutoff:3.500A)
removed outlier: 5.410A pdb=" N GLU F 378 " --> pdb=" O PHE F 385 " (cutoff:3.500A)
removed outlier: 6.920A pdb=" N PHE F 385 " --> pdb=" O GLU F 378 " (cutoff:3.500A)
removed outlier: 7.070A pdb=" N VAL F 429 " --> pdb=" O PHE F 470 " (cutoff:3.500A)
removed outlier: 6.784A pdb=" N PHE F 470 " --> pdb=" O VAL F 429 " (cutoff:3.500A)
removed outlier: 6.643A pdb=" N TRP F 431 " --> pdb=" O ALA F 468 " (cutoff:3.500A)
removed outlier: 6.510A pdb=" N ALA F 468 " --> pdb=" O TRP F 431 " (cutoff:3.500A)
removed outlier: 6.881A pdb=" N ILE F 433 " --> pdb=" O ALA F 466 " (cutoff:3.500A)
removed outlier: 6.979A pdb=" N ALA F 466 " --> pdb=" O ILE F 433 " (cutoff:3.500A)
removed outlier: 6.788A pdb=" N GLY F 435 " --> pdb=" O VAL F 464 " (cutoff:3.500A)
removed outlier: 6.799A pdb=" N VAL F 464 " --> pdb=" O GLY F 435 " (cutoff:3.500A)
removed outlier: 6.973A pdb=" N ARG F 437 " --> pdb=" O LYS F 462 " (cutoff:3.500A)
removed outlier: 6.870A pdb=" N LYS F 462 " --> pdb=" O ARG F 437 " (cutoff:3.500A)
removed outlier: 6.959A pdb=" N ASP F 439 " --> pdb=" O ARG F 460 " (cutoff:3.500A)
removed outlier: 6.920A pdb=" N ARG F 460 " --> pdb=" O ASP F 439 " (cutoff:3.500A)
removed outlier: 6.717A pdb=" N SER F 441 " --> pdb=" O LYS F 458 " (cutoff:3.500A)
removed outlier: 6.464A pdb=" N LYS F 458 " --> pdb=" O SER F 441 " (cutoff:3.500A)
removed outlier: 4.485A pdb=" N LEU F 443 " --> pdb=" O GLU F 456 " (cutoff:3.500A)
Processing sheet with id=AC3, first strand: chain 'F' and resid 527 through 529
952 hydrogen bonds defined for protein.
2628 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: 13.57
Time building geometry restraints manager: 32.23 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
0.83 - 1.04: 17527
1.04 - 1.25: 3241
1.25 - 1.46: 7465
1.46 - 1.67: 8202
1.67 - 1.88: 52
Bond restraints: 36487
Sorted by residual:
bond pdb=" CB CYS D 33 "
pdb=" SG CYS D 33 "
ideal model delta sigma weight residual
1.808 1.877 -0.069 3.30e-02 9.18e+02 4.39e+00
bond pdb=" CB PRO D 383 "
pdb=" CG PRO D 383 "
ideal model delta sigma weight residual
1.492 1.404 0.088 5.00e-02 4.00e+02 3.12e+00
bond pdb=" CB TYR F 405 "
pdb=" CG TYR F 405 "
ideal model delta sigma weight residual
1.512 1.483 0.029 2.20e-02 2.07e+03 1.71e+00
bond pdb=" CA SER C 95 "
pdb=" CB SER C 95 "
ideal model delta sigma weight residual
1.534 1.512 0.021 1.78e-02 3.16e+03 1.45e+00
bond pdb=" CA TYR C 58 "
pdb=" CB TYR C 58 "
ideal model delta sigma weight residual
1.535 1.513 0.022 2.09e-02 2.29e+03 1.12e+00
... (remaining 36482 not shown)
Histogram of bond angle deviations from ideal:
98.30 - 105.45: 289
105.45 - 112.61: 39866
112.61 - 119.76: 10082
119.76 - 126.91: 14916
126.91 - 134.07: 192
Bond angle restraints: 65345
Sorted by residual:
angle pdb=" C SER D 17 "
pdb=" N GLY D 18 "
pdb=" CA GLY D 18 "
ideal model delta sigma weight residual
119.92 124.13 -4.21 9.60e-01 1.09e+00 1.92e+01
angle pdb=" N CYS E 201 "
pdb=" CA CYS E 201 "
pdb=" C CYS E 201 "
ideal model delta sigma weight residual
110.42 115.79 -5.37 1.46e+00 4.69e-01 1.35e+01
angle pdb=" N GLY D 32 "
pdb=" CA GLY D 32 "
pdb=" C GLY D 32 "
ideal model delta sigma weight residual
113.18 104.53 8.65 2.37e+00 1.78e-01 1.33e+01
angle pdb=" N ASP F 162 "
pdb=" CA ASP F 162 "
pdb=" C ASP F 162 "
ideal model delta sigma weight residual
114.12 109.25 4.87 1.39e+00 5.18e-01 1.23e+01
angle pdb=" C SER D 30 "
pdb=" N GLY D 31 "
pdb=" CA GLY D 31 "
ideal model delta sigma weight residual
121.60 131.08 -9.48 2.86e+00 1.22e-01 1.10e+01
... (remaining 65340 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 17.98: 13361
17.98 - 35.96: 995
35.96 - 53.94: 222
53.94 - 71.93: 61
71.93 - 89.91: 14
Dihedral angle restraints: 14653
sinusoidal: 6459
harmonic: 8194
Sorted by residual:
dihedral pdb=" CA LEU E 302 "
pdb=" C LEU E 302 "
pdb=" N ALA E 303 "
pdb=" CA ALA E 303 "
ideal model delta harmonic sigma weight residual
180.00 155.30 24.70 0 5.00e+00 4.00e-02 2.44e+01
dihedral pdb=" CA MET E 203 "
pdb=" C MET E 203 "
pdb=" N SER E 204 "
pdb=" CA SER E 204 "
ideal model delta harmonic sigma weight residual
180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01
dihedral pdb=" CA ASP A 127 "
pdb=" C ASP A 127 "
pdb=" N PHE A 128 "
pdb=" CA PHE A 128 "
ideal model delta harmonic sigma weight residual
-180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01
... (remaining 14650 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.036: 1764
0.036 - 0.073: 625
0.073 - 0.109: 189
0.109 - 0.146: 115
0.146 - 0.182: 4
Chirality restraints: 2697
Sorted by residual:
chirality pdb=" CA ILE E 159 "
pdb=" N ILE E 159 "
pdb=" C ILE E 159 "
pdb=" CB ILE E 159 "
both_signs ideal model delta sigma weight residual
False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.28e-01
chirality pdb=" CA VAL D 29 "
pdb=" N VAL D 29 "
pdb=" C VAL D 29 "
pdb=" CB VAL D 29 "
both_signs ideal model delta sigma weight residual
False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.22e-01
chirality pdb=" CA ILE B 187 "
pdb=" N ILE B 187 "
pdb=" C ILE B 187 "
pdb=" CB ILE B 187 "
both_signs ideal model delta sigma weight residual
False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.01e-01
... (remaining 2694 not shown)
Planarity restraints: 5790
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CA GLU D 440 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01
pdb=" C GLU D 440 " -0.058 2.00e-02 2.50e+03
pdb=" O GLU D 440 " 0.022 2.00e-02 2.50e+03
pdb=" N LYS D 441 " 0.020 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA PHE E 153 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.09e+01
pdb=" C PHE E 153 " 0.057 2.00e-02 2.50e+03
pdb=" O PHE E 153 " -0.021 2.00e-02 2.50e+03
pdb=" N GLU E 154 " -0.019 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA TYR D 324 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01
pdb=" C TYR D 324 " -0.056 2.00e-02 2.50e+03
pdb=" O TYR D 324 " 0.021 2.00e-02 2.50e+03
pdb=" N GLU D 325 " 0.019 2.00e-02 2.50e+03
... (remaining 5787 not shown)
Histogram of nonbonded interaction distances:
1.43 - 2.07: 772
2.07 - 2.70: 58582
2.70 - 3.33: 104557
3.33 - 3.97: 136206
3.97 - 4.60: 210956
Nonbonded interactions: 511073
Sorted by model distance:
nonbonded pdb=" O HIS F 75 "
pdb=" H GLY F 124 "
model vdw
1.434 1.850
nonbonded pdb=" OD2 ASP F 528 "
pdb=" H TYR F 577 "
model vdw
1.483 1.850
nonbonded pdb="HE22 GLN F 364 "
pdb=" O PRO F 408 "
model vdw
1.485 1.850
nonbonded pdb=" O VAL D 29 "
pdb="HE22 GLN E 172 "
model vdw
1.489 1.850
nonbonded pdb=" OE1 GLU D 167 "
pdb=" H GLU D 167 "
model vdw
1.523 1.850
... (remaining 511068 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
reference = (chain 'A' and (resid 1 through 89 or (resid 90 and (name N or name CA or name C \
or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \
or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name HD1 \
or name HD2 or name HE1 or name HE2)) or resid 91 through 340))
selection = (chain 'B' and (resid 1 through 89 or (resid 90 and (name N or name CA or name C \
or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \
or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name HD1 \
or name HD2 or name HE1 or name HE2)) or resid 91 through 340))
selection = chain 'C'
}
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
Set to: electron
Number of scattering types: 5
Type Number sf(0) Gaussians
S 27 5.16 5
C 11613 2.51 5
N 3196 2.21 5
O 3707 1.98 5
H 17527 0.53 5
sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=0.20 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: 1.130
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: 0.560
Extract box with map and model: 7.650
Check model and map are aligned: 0.540
Convert atoms to be neutral: 0.280
Process input model: 111.720
Find NCS groups from input model: 1.090
Set up NCS constraints: 0.100
Set refine NCS operators: 0.000
Set scattering table: 0.020
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:2.720
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 125.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4864
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 : 0.003 0.088 18960 Z= 0.218
Angle : 0.698 9.478 25744 Z= 0.401
Chirality : 0.046 0.182 2697
Planarity : 0.005 0.054 3458
Dihedral : 14.513 89.907 6748
Min Nonbonded Distance : 1.833
Molprobity Statistics.
All-atom Clashscore : 11.06
Ramachandran Plot:
Outliers : 0.13 %
Allowed : 4.85 %
Favored : 95.02 %
Rotamer Outliers : 3.66 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.27 %
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: -1.84 (0.16), residues: 2401
helix: -2.33 (0.25), residues: 248
sheet: -0.58 (0.15), residues: 1069
loop : -1.52 (0.17), residues: 1084
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 90 is missing expected H atoms. Skipping.
Residue THR 16 is missing expected H atoms. Skipping.
Residue SER 17 is missing expected H atoms. Skipping.
Residue THR 25 is missing expected H atoms. Skipping.
Residue ILE 27 is missing expected H atoms. Skipping.
Residue VAL 29 is missing expected H atoms. Skipping.
Residue SER 30 is missing expected H atoms. Skipping.
Residue SER 50 is missing expected H atoms. Skipping.
Residue SER 52 is missing expected H atoms. Skipping.
Residue ILE 54 is missing expected H atoms. Skipping.
Evaluate side-chains
560 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 68
poor density : 492
time to evaluate : 2.952
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 68
outliers final: 35
residues processed: 547
average time/residue: 0.7069
time to fit residues: 571.7193
Evaluate side-chains
471 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 35
poor density : 436
time to evaluate : 2.614
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 35
outliers final: 7
residues processed: 35
average time/residue: 0.5914
time to fit residues: 35.4937
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 202 optimal weight: 4.9990
chunk 181 optimal weight: 9.9990
chunk 100 optimal weight: 3.9990
chunk 62 optimal weight: 2.9990
chunk 122 optimal weight: 10.0000
chunk 97 optimal weight: 4.9990
chunk 188 optimal weight: 7.9990
chunk 72 optimal weight: 0.9990
chunk 114 optimal weight: 50.0000
chunk 140 optimal weight: 10.0000
chunk 217 optimal weight: 3.9990
overall best weight: 3.3990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 246 ASN
E 290 ASN
E 334 ASN
** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 347 GLN
F 368 HIS
** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5196
moved from start: 0.2888
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.006 0.080 18960 Z= 0.414
Angle : 0.765 9.318 25744 Z= 0.432
Chirality : 0.047 0.174 2697
Planarity : 0.007 0.113 3458
Dihedral : 5.540 26.218 2678
Min Nonbonded Distance : 1.734
Molprobity Statistics.
All-atom Clashscore : 24.62
Ramachandran Plot:
Outliers : 0.08 %
Allowed : 3.68 %
Favored : 96.23 %
Rotamer Outliers : 0.47 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.27 %
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: -1.16 (0.16), residues: 2401
helix: -0.33 (0.29), residues: 256
sheet: -0.36 (0.15), residues: 1109
loop : -1.23 (0.19), residues: 1036
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 90 is missing expected H atoms. Skipping.
Residue THR 16 is missing expected H atoms. Skipping.
Residue SER 17 is missing expected H atoms. Skipping.
Residue THR 25 is missing expected H atoms. Skipping.
Residue ILE 27 is missing expected H atoms. Skipping.
Residue VAL 29 is missing expected H atoms. Skipping.
Residue SER 30 is missing expected H atoms. Skipping.
Residue SER 50 is missing expected H atoms. Skipping.
Residue SER 52 is missing expected H atoms. Skipping.
Residue ILE 54 is missing expected H atoms. Skipping.
Evaluate side-chains
468 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 7
poor density : 461
time to evaluate : 2.747
Fit side-chains
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 7
outliers final: 4
residues processed: 466
average time/residue: 0.6981
time to fit residues: 484.6007
Evaluate side-chains
427 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 4
poor density : 423
time to evaluate : 2.625
Switching outliers to nearest non-outliers
outliers start: 4
outliers final: 0
residues processed: 4
average time/residue: 0.6755
time to fit residues: 7.5307
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 121 optimal weight: 9.9990
chunk 67 optimal weight: 0.9990
chunk 181 optimal weight: 0.9990
chunk 148 optimal weight: 6.9990
chunk 60 optimal weight: 3.9990
chunk 218 optimal weight: 2.9990
chunk 235 optimal weight: 0.9980
chunk 194 optimal weight: 1.9990
chunk 216 optimal weight: 0.6980
chunk 74 optimal weight: 0.9980
chunk 175 optimal weight: 9.9990
overall best weight: 0.9384
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 252 ASN
C 21 HIS
D 281 HIS
D 315 HIS
D 375 GLN
E 78 GLN
E 87 GLN
Total number of N/Q/H flips: 7
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5060
moved from start: 0.3231
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.040 18960 Z= 0.174
Angle : 0.551 7.575 25744 Z= 0.306
Chirality : 0.044 0.148 2697
Planarity : 0.004 0.050 3458
Dihedral : 4.949 29.611 2678
Min Nonbonded Distance : 1.764
Molprobity Statistics.
All-atom Clashscore : 12.73
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.80 %
Favored : 97.20 %
Rotamer Outliers : 0.16 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.27 %
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: -0.57 (0.17), residues: 2401
helix: 1.32 (0.33), residues: 234
sheet: -0.15 (0.15), residues: 1076
loop : -0.91 (0.19), residues: 1091
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 90 is missing expected H atoms. Skipping.
Residue THR 16 is missing expected H atoms. Skipping.
Residue SER 17 is missing expected H atoms. Skipping.
Residue THR 25 is missing expected H atoms. Skipping.
Residue ILE 27 is missing expected H atoms. Skipping.
Residue VAL 29 is missing expected H atoms. Skipping.
Residue SER 30 is missing expected H atoms. Skipping.
Residue SER 50 is missing expected H atoms. Skipping.
Residue SER 52 is missing expected H atoms. Skipping.
Residue ILE 54 is missing expected H atoms. Skipping.
Evaluate side-chains
445 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 444
time to evaluate : 2.675
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: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 1
outliers final: 0
residues processed: 445
average time/residue: 0.6849
time to fit residues: 451.8885
Evaluate side-chains
418 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 418
time to evaluate : 2.648
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 3.4899
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 215 optimal weight: 4.9990
chunk 164 optimal weight: 9.9990
chunk 113 optimal weight: 7.9990
chunk 24 optimal weight: 2.9990
chunk 104 optimal weight: 20.0000
chunk 146 optimal weight: 2.9990
chunk 219 optimal weight: 2.9990
chunk 231 optimal weight: 0.8980
chunk 114 optimal weight: 50.0000
chunk 207 optimal weight: 5.9990
chunk 62 optimal weight: 0.3980
overall best weight: 2.0586
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 GLN
** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 281 HIS
** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5167
moved from start: 0.3758
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.074 18960 Z= 0.268
Angle : 0.596 7.589 25744 Z= 0.334
Chirality : 0.044 0.148 2697
Planarity : 0.005 0.056 3458
Dihedral : 5.000 29.954 2678
Min Nonbonded Distance : 1.777
Molprobity Statistics.
All-atom Clashscore : 17.63
Ramachandran Plot:
Outliers : 0.04 %
Allowed : 3.93 %
Favored : 96.03 %
Rotamer Outliers : 0.16 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.27 %
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: -0.67 (0.17), residues: 2401
helix: 0.95 (0.31), residues: 255
sheet: -0.20 (0.15), residues: 1097
loop : -0.96 (0.19), residues: 1049
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 90 is missing expected H atoms. Skipping.
Residue THR 16 is missing expected H atoms. Skipping.
Residue SER 17 is missing expected H atoms. Skipping.
Residue THR 25 is missing expected H atoms. Skipping.
Residue ILE 27 is missing expected H atoms. Skipping.
Residue VAL 29 is missing expected H atoms. Skipping.
Residue SER 30 is missing expected H atoms. Skipping.
Residue SER 50 is missing expected H atoms. Skipping.
Residue SER 52 is missing expected H atoms. Skipping.
Residue ILE 54 is missing expected H atoms. Skipping.
Evaluate side-chains
449 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 448
time to evaluate : 2.664
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: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 1
outliers final: 1
residues processed: 449
average time/residue: 0.6914
time to fit residues: 462.3943
Evaluate side-chains
423 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 422
time to evaluate : 2.659
Switching outliers to nearest non-outliers
outliers start: 1
outliers final: 0
residues processed: 1
average time/residue: 0.3804
time to fit residues: 4.2203
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 193 optimal weight: 4.9990
chunk 131 optimal weight: 20.0000
chunk 3 optimal weight: 7.9990
chunk 172 optimal weight: 9.9990
chunk 95 optimal weight: 0.8980
chunk 197 optimal weight: 6.9990
chunk 160 optimal weight: 7.9990
chunk 0 optimal weight: 3.9990
chunk 118 optimal weight: 6.9990
chunk 208 optimal weight: 7.9990
chunk 58 optimal weight: 0.7980
overall best weight: 3.5386
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 52 ASN
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 224 ASN
** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 236 ASN
D 409 GLN
** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 521 GLN
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5362
moved from start: 0.4772
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.007 0.140 18960 Z= 0.421
Angle : 0.762 10.784 25744 Z= 0.432
Chirality : 0.047 0.205 2697
Planarity : 0.006 0.093 3458
Dihedral : 5.801 36.047 2678
Min Nonbonded Distance : 1.697
Molprobity Statistics.
All-atom Clashscore : 31.97
Ramachandran Plot:
Outliers : 0.04 %
Allowed : 6.86 %
Favored : 93.10 %
Rotamer Outliers : 0.26 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.27 %
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: -1.33 (0.17), residues: 2401
helix: 0.14 (0.30), residues: 255
sheet: -0.47 (0.15), residues: 1131
loop : -1.55 (0.19), residues: 1015
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 90 is missing expected H atoms. Skipping.
Residue THR 16 is missing expected H atoms. Skipping.
Residue SER 17 is missing expected H atoms. Skipping.
Residue THR 25 is missing expected H atoms. Skipping.
Residue ILE 27 is missing expected H atoms. Skipping.
Residue VAL 29 is missing expected H atoms. Skipping.
Residue SER 30 is missing expected H atoms. Skipping.
Residue SER 50 is missing expected H atoms. Skipping.
Residue SER 52 is missing expected H atoms. Skipping.
Residue ILE 54 is missing expected H atoms. Skipping.
Evaluate side-chains
473 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 3
poor density : 470
time to evaluate : 2.466
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: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 3
outliers final: 1
residues processed: 472
average time/residue: 0.7027
time to fit residues: 497.4531
Evaluate side-chains
435 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 434
time to evaluate : 2.645
Switching outliers to nearest non-outliers
outliers start: 1
outliers final: 0
residues processed: 1
average time/residue: 0.3815
time to fit residues: 4.2156
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 78 optimal weight: 3.9990
chunk 208 optimal weight: 0.9980
chunk 45 optimal weight: 2.9990
chunk 136 optimal weight: 0.8980
chunk 57 optimal weight: 2.9990
chunk 232 optimal weight: 0.1980
chunk 192 optimal weight: 4.9990
chunk 107 optimal weight: 10.0000
chunk 19 optimal weight: 4.9990
chunk 76 optimal weight: 1.9990
chunk 121 optimal weight: 20.0000
overall best weight: 1.4184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 ASN
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5224
moved from start: 0.4927
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.052 18960 Z= 0.217
Angle : 0.581 6.614 25744 Z= 0.326
Chirality : 0.045 0.176 2697
Planarity : 0.005 0.081 3458
Dihedral : 5.247 29.736 2678
Min Nonbonded Distance : 1.759
Molprobity Statistics.
All-atom Clashscore : 17.33
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.06 %
Favored : 95.94 %
Rotamer Outliers : 0.10 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.27 %
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: -0.89 (0.17), residues: 2401
helix: 1.31 (0.33), residues: 234
sheet: -0.30 (0.15), residues: 1117
loop : -1.28 (0.19), residues: 1050
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 90 is missing expected H atoms. Skipping.
Residue THR 16 is missing expected H atoms. Skipping.
Residue SER 17 is missing expected H atoms. Skipping.
Residue THR 25 is missing expected H atoms. Skipping.
Residue ILE 27 is missing expected H atoms. Skipping.
Residue VAL 29 is missing expected H atoms. Skipping.
Residue SER 30 is missing expected H atoms. Skipping.
Residue SER 50 is missing expected H atoms. Skipping.
Residue SER 52 is missing expected H atoms. Skipping.
Residue ILE 54 is missing expected H atoms. Skipping.
Evaluate side-chains
463 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 463
time to evaluate : 2.634
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: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 0
outliers final: 0
residues processed: 463
average time/residue: 0.7097
time to fit residues: 489.8531
Evaluate side-chains
431 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 431
time to evaluate : 2.555
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 3.4287
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 223 optimal weight: 2.9990
chunk 26 optimal weight: 4.9990
chunk 132 optimal weight: 1.9990
chunk 169 optimal weight: 8.9990
chunk 131 optimal weight: 8.9990
chunk 195 optimal weight: 7.9990
chunk 129 optimal weight: 4.9990
chunk 231 optimal weight: 3.9990
chunk 144 optimal weight: 40.0000
chunk 141 optimal weight: 2.9990
chunk 106 optimal weight: 5.9990
overall best weight: 3.3990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5394
moved from start: 0.5527
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.006 0.119 18960 Z= 0.416
Angle : 0.746 9.423 25744 Z= 0.422
Chirality : 0.047 0.321 2697
Planarity : 0.006 0.073 3458
Dihedral : 5.795 37.081 2678
Min Nonbonded Distance : 1.682
Molprobity Statistics.
All-atom Clashscore : 32.16
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 7.95 %
Favored : 92.05 %
Rotamer Outliers : 0.10 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.27 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.04 %
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: -1.44 (0.17), residues: 2401
helix: 0.20 (0.31), residues: 252
sheet: -0.57 (0.15), residues: 1102
loop : -1.59 (0.18), residues: 1047
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 90 is missing expected H atoms. Skipping.
Residue THR 16 is missing expected H atoms. Skipping.
Residue SER 17 is missing expected H atoms. Skipping.
Residue THR 25 is missing expected H atoms. Skipping.
Residue ILE 27 is missing expected H atoms. Skipping.
Residue VAL 29 is missing expected H atoms. Skipping.
Residue SER 30 is missing expected H atoms. Skipping.
Residue SER 50 is missing expected H atoms. Skipping.
Residue SER 52 is missing expected H atoms. Skipping.
Residue ILE 54 is missing expected H atoms. Skipping.
Evaluate side-chains
464 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 464
time to evaluate : 2.778
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: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 0
outliers final: 0
residues processed: 464
average time/residue: 0.7122
time to fit residues: 490.8489
Evaluate side-chains
433 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 433
time to evaluate : 2.834
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 3.8742
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 143 optimal weight: 4.9990
chunk 92 optimal weight: 0.8980
chunk 138 optimal weight: 2.9990
chunk 69 optimal weight: 3.9990
chunk 45 optimal weight: 3.9990
chunk 44 optimal weight: 4.9990
chunk 147 optimal weight: 0.9990
chunk 157 optimal weight: 9.9990
chunk 114 optimal weight: 50.0000
chunk 21 optimal weight: 4.9990
chunk 181 optimal weight: 9.9990
overall best weight: 2.5788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5343
moved from start: 0.5769
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.005 0.068 18960 Z= 0.306
Angle : 0.655 8.324 25744 Z= 0.368
Chirality : 0.045 0.165 2697
Planarity : 0.005 0.109 3458
Dihedral : 5.655 32.316 2678
Min Nonbonded Distance : 1.703
Molprobity Statistics.
All-atom Clashscore : 23.48
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 6.57 %
Favored : 93.43 %
Rotamer Outliers : 0.10 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.27 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.04 %
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: -1.34 (0.17), residues: 2401
helix: 0.45 (0.32), residues: 252
sheet: -0.54 (0.15), residues: 1115
loop : -1.54 (0.18), residues: 1034
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 90 is missing expected H atoms. Skipping.
Residue THR 16 is missing expected H atoms. Skipping.
Residue SER 17 is missing expected H atoms. Skipping.
Residue THR 25 is missing expected H atoms. Skipping.
Residue ILE 27 is missing expected H atoms. Skipping.
Residue VAL 29 is missing expected H atoms. Skipping.
Residue SER 30 is missing expected H atoms. Skipping.
Residue SER 50 is missing expected H atoms. Skipping.
Residue SER 52 is missing expected H atoms. Skipping.
Residue ILE 54 is missing expected H atoms. Skipping.
Evaluate side-chains
454 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 454
time to evaluate : 2.683
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: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 0
outliers final: 0
residues processed: 454
average time/residue: 0.7226
time to fit residues: 487.2883
Evaluate side-chains
433 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 433
time to evaluate : 2.694
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 3.4936
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 210 optimal weight: 3.9990
chunk 221 optimal weight: 4.9990
chunk 202 optimal weight: 0.9990
chunk 215 optimal weight: 6.9990
chunk 129 optimal weight: 5.9990
chunk 93 optimal weight: 0.9980
chunk 169 optimal weight: 9.9990
chunk 66 optimal weight: 1.9990
chunk 194 optimal weight: 3.9990
chunk 203 optimal weight: 4.9990
chunk 214 optimal weight: 4.9990
overall best weight: 2.3988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 52 ASN
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5356
moved from start: 0.6039
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.005 0.075 18960 Z= 0.309
Angle : 0.649 8.186 25744 Z= 0.367
Chirality : 0.045 0.173 2697
Planarity : 0.005 0.083 3458
Dihedral : 5.621 30.649 2678
Min Nonbonded Distance : 1.707
Molprobity Statistics.
All-atom Clashscore : 24.79
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 7.82 %
Favored : 92.18 %
Rotamer Outliers : 0.16 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.27 %
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: -1.38 (0.17), residues: 2401
helix: 0.52 (0.32), residues: 252
sheet: -0.58 (0.15), residues: 1112
loop : -1.58 (0.18), residues: 1037
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 90 is missing expected H atoms. Skipping.
Residue THR 16 is missing expected H atoms. Skipping.
Residue SER 17 is missing expected H atoms. Skipping.
Residue THR 25 is missing expected H atoms. Skipping.
Residue ILE 27 is missing expected H atoms. Skipping.
Residue VAL 29 is missing expected H atoms. Skipping.
Residue SER 30 is missing expected H atoms. Skipping.
Residue SER 50 is missing expected H atoms. Skipping.
Residue SER 52 is missing expected H atoms. Skipping.
Residue ILE 54 is missing expected H atoms. Skipping.
Evaluate side-chains
458 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 457
time to evaluate : 2.693
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: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 1
outliers final: 0
residues processed: 457
average time/residue: 0.7407
time to fit residues: 503.1600
Evaluate side-chains
434 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 434
time to evaluate : 2.823
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 3.6344
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 141 optimal weight: 0.5980
chunk 227 optimal weight: 0.5980
chunk 139 optimal weight: 3.9990
chunk 108 optimal weight: 40.0000
chunk 158 optimal weight: 9.9990
chunk 239 optimal weight: 4.9990
chunk 220 optimal weight: 1.9990
chunk 190 optimal weight: 4.9990
chunk 19 optimal weight: 0.9980
chunk 147 optimal weight: 0.8980
chunk 116 optimal weight: 5.9990
overall best weight: 1.0182
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5264
moved from start: 0.6063
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.059 18960 Z= 0.193
Angle : 0.574 6.039 25744 Z= 0.320
Chirality : 0.045 0.183 2697
Planarity : 0.005 0.076 3458
Dihedral : 5.329 27.899 2678
Min Nonbonded Distance : 1.725
Molprobity Statistics.
All-atom Clashscore : 17.33
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.56 %
Favored : 95.44 %
Rotamer Outliers : 0.10 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.27 %
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: -1.02 (0.17), residues: 2401
helix: 1.42 (0.34), residues: 234
sheet: -0.46 (0.15), residues: 1112
loop : -1.32 (0.19), residues: 1055
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4802 Ramachandran restraints generated.
2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 90 is missing expected H atoms. Skipping.
Residue THR 16 is missing expected H atoms. Skipping.
Residue SER 17 is missing expected H atoms. Skipping.
Residue THR 25 is missing expected H atoms. Skipping.
Residue ILE 27 is missing expected H atoms. Skipping.
Residue VAL 29 is missing expected H atoms. Skipping.
Residue SER 30 is missing expected H atoms. Skipping.
Residue SER 50 is missing expected H atoms. Skipping.
Residue SER 52 is missing expected H atoms. Skipping.
Residue ILE 54 is missing expected H atoms. Skipping.
Evaluate side-chains
461 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 461
time to evaluate : 2.686
Fit side-chains
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outliers start: 0
outliers final: 0
residues processed: 461
average time/residue: 0.7123
time to fit residues: 487.4707
Evaluate side-chains
435 residues out of total 1900 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 435
time to evaluate : 2.916
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 3.6577
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
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XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 151 optimal weight: 6.9990
chunk 202 optimal weight: 1.9990
chunk 58 optimal weight: 1.9990
chunk 175 optimal weight: 10.0000
chunk 28 optimal weight: 2.9990
chunk 52 optimal weight: 0.8980
chunk 190 optimal weight: 0.8980
chunk 79 optimal weight: 3.9990
chunk 195 optimal weight: 1.9990
chunk 24 optimal weight: 2.9990
chunk 35 optimal weight: 4.9990
overall best weight: 1.5586
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NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
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ADP refinement
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|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4782 r_free = 0.4782 target = 0.218729 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.168646 restraints weight = 177858.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.180033 restraints weight = 90077.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.186905 restraints weight = 50474.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.4422
-------------------------------------------------------------------------------
Occupancy refinement
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r_start: 0.4782
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4782 r_free = 0.4782 target_work(ls_wunit_k1) = 0.219 |
| occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4781 r_free = 0.4781 target_work(ls_wunit_k1) = 0.219 |
| occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 |
|-----------------------------------------------------------------------------|
r_final: 0.4781
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5338
moved from start: 0.6205
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.072 18960 Z= 0.228
Angle : 0.579 6.493 25744 Z= 0.325
Chirality : 0.044 0.171 2697
Planarity : 0.004 0.079 3458
Dihedral : 5.261 29.954 2678
Min Nonbonded Distance : 1.717
Molprobity Statistics.
All-atom Clashscore : 19.21
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 6.32 %
Favored : 93.68 %
Rotamer Outliers : 0.10 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.27 %
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: -1.04 (0.17), residues: 2401
helix: 1.45 (0.34), residues: 234
sheet: -0.47 (0.15), residues: 1104
loop : -1.34 (0.18), residues: 1063
===============================================================================
Job complete
usr+sys time: 9194.11 seconds
wall clock time: 163 minutes 13.66 seconds (9793.66 seconds total)