Starting phenix.real_space_refine (version: dev)
on Mon Feb 27 19:50:12 2023 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb4_20286/02_2023/6pb4_20286_trim_updated.pdb
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb4_20286/02_2023/6pb4_20286.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=4.35
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb4_20286/02_2023/6pb4_20286.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb4_20286/02_2023/6pb4_20286.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb4_20286/02_2023/6pb4_20286_trim_updated.pdb"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb4_20286/02_2023/6pb4_20286_trim_updated.pdb"
}
resolution = 4.35
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= -0.009 sd= 0.338
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
Process input model
Symmetric amino acids flipped
Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C ARG 268": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "C ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "C TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D ARG 1355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "F PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Time to flip residues: 0.08s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib"
Total number of atoms: 69922
Number of models: 1
Model: ""
Number of chains: 14
Chain: "A"
Number of atoms: 3599
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 230, 3599
Classifications: {'peptide': 230}
Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220}
Chain: "B"
Number of atoms: 3556
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 228, 3556
Classifications: {'peptide': 228}
Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218}
Chain: "C"
Number of atoms: 21151
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1340, 21151
Classifications: {'peptide': 1340}
Modifications used: {'COO': 1}
Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283}
Chain: "D"
Number of atoms: 21012
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1337, 21012
Classifications: {'peptide': 1337}
Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1281}
Chain breaks: 2
Chain: "E"
Number of atoms: 1261
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 79, 1261
Classifications: {'peptide': 79}
Link IDs: {'PTRANS': 2, 'TRANS': 76}
Chain: "F"
Number of atoms: 7918
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 483, 7918
Classifications: {'peptide': 483}
Link IDs: {'PTRANS': 15, 'TRANS': 467}
Chain breaks: 1
Chain: "G"
Number of atoms: 3156
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 197, 3156
Classifications: {'peptide': 197}
Link IDs: {'PTRANS': 4, 'TRANS': 192}
Chain: "H"
Number of atoms: 3156
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 197, 3156
Classifications: {'peptide': 197}
Link IDs: {'PTRANS': 4, 'TRANS': 192}
Chain: "1"
Number of atoms: 2481
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 78, 2481
Classifications: {'DNA': 78}
Modifications used: {'3*END': 1}
Link IDs: {'rna3p': 77}
Chain: "2"
Number of atoms: 2485
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 78, 2485
Classifications: {'DNA': 78}
Modifications used: {'3*END': 1}
Link IDs: {'rna3p': 77}
Chain: "3"
Number of atoms: 100
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 100
Unusual residues: {'GTP': 1}
Classifications: {'RNA': 2, 'undetermined': 1}
Modifications used: {'3*END': 1, 'rna3p_pur': 2}
Link IDs: {'rna3p': 1, None: 1}
Not linked:
pdbres="GTP 3 1 "
pdbres=" A 3 2 "
Chain: "D"
Number of atoms: 3
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 3
Unusual residues: {' MG': 1, ' ZN': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Chain: "G"
Number of atoms: 22
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 22
Classifications: {'RNA': 1}
Modifications used: {'rna3p': 1}
Chain: "H"
Number of atoms: 22
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 22
Classifications: {'RNA': 1}
Modifications used: {'rna3p': 1}
List of CYS excluded from plausible disulfide bonds:
(reason: may participate in coordination)
ATOM 29206 SG CYS D 70 108.252 108.311 126.147 1.00 20.00 S
ATOM 29235 SG CYS D 72 104.923 110.858 128.106 1.00 20.00 S
ATOM 41047 SG CYS D 814 107.674 46.822 91.527 1.00 20.00 S
ATOM 42184 SG CYS D 888 105.694 49.603 91.940 1.00 20.00 S
ATOM 42276 SG CYS D 895 108.730 49.042 89.185 1.00 20.00 S
ATOM 42313 SG CYS D 898 105.720 47.290 87.924 1.00 20.00 S
Time building chain proxies: 24.06, per 1000 atoms: 0.34
Number of scatterers: 69922
At special positions: 0
Unit cell: (202.5, 178.2, 192.6, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 8
Type Number sf(0)
Zn 2 29.99
S 147 16.00
P 163 15.00
Mg 1 11.99
O 7142 8.00
N 6293 7.00
C 21765 6.00
H 34409 1.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
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=1, symmetry=0
Number of additional bonds: simple=1, symmetry=0
Coordination:
Other bonds:
Time building additional restraints: 48.19
Conformation dependent library (CDL) restraints added in 4.1 seconds
Dynamic metal coordination
Zn2+ tetrahedral coordination
pdb=" ZN D1501 "
pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 "
pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 "
pdb=" ZN D1502 "
pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 "
pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 "
pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 "
pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 "
Number of angles added : 6
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 7596
Finding SS restraints...
running ksdssp...
Secondary structure from input PDB file:
139 helices and 38 sheets defined
35.8% alpha, 9.0% beta
45 base pairs and 112 stacking pairs defined.
Time for finding SS restraints: 25.98
Creating SS restraints...
Processing helix chain 'A' and resid 35 through 49
removed outlier: 3.523A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A)
removed outlier: 3.838A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A)
Processing helix chain 'A' and resid 78 through 86
Processing helix chain 'A' and resid 112 through 114
No H-bonds generated for 'chain 'A' and resid 112 through 114'
Processing helix chain 'A' and resid 156 through 161
Processing helix chain 'A' and resid 213 through 232
removed outlier: 4.249A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A)
removed outlier: 3.819A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A)
Processing helix chain 'B' and resid 36 through 49
Processing helix chain 'B' and resid 78 through 86
Processing helix chain 'B' and resid 155 through 161
Processing helix chain 'B' and resid 213 through 227
Processing helix chain 'C' and resid 5 through 9
Processing helix chain 'C' and resid 29 through 39
Processing helix chain 'C' and resid 48 through 56
Processing helix chain 'C' and resid 83 through 88
Processing helix chain 'C' and resid 206 through 212
Processing helix chain 'C' and resid 217 through 224
removed outlier: 4.258A pdb=" N LEU C 223 " --> pdb=" O GLN C 219 " (cutoff:3.500A)
Processing helix chain 'C' and resid 271 through 280
Processing helix chain 'C' and resid 289 through 292
Processing helix chain 'C' and resid 319 through 328
Processing helix chain 'C' and resid 347 through 353
Processing helix chain 'C' and resid 359 through 370
Processing helix chain 'C' and resid 378 through 389
removed outlier: 3.663A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A)
Processing helix chain 'C' and resid 399 through 408
Processing helix chain 'C' and resid 422 through 437
Processing helix chain 'C' and resid 448 through 450
No H-bonds generated for 'chain 'C' and resid 448 through 450'
Processing helix chain 'C' and resid 456 through 481
removed outlier: 4.360A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A)
removed outlier: 3.633A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A)
Processing helix chain 'C' and resid 496 through 505
Processing helix chain 'C' and resid 520 through 527
Processing helix chain 'C' and resid 545 through 548
No H-bonds generated for 'chain 'C' and resid 545 through 548'
Processing helix chain 'C' and resid 552 through 554
No H-bonds generated for 'chain 'C' and resid 552 through 554'
Processing helix chain 'C' and resid 610 through 613
No H-bonds generated for 'chain 'C' and resid 610 through 613'
Processing helix chain 'C' and resid 663 through 666
No H-bonds generated for 'chain 'C' and resid 663 through 666'
Processing helix chain 'C' and resid 671 through 673
No H-bonds generated for 'chain 'C' and resid 671 through 673'
Processing helix chain 'C' and resid 676 through 685
Processing helix chain 'C' and resid 705 through 708
No H-bonds generated for 'chain 'C' and resid 705 through 708'
Processing helix chain 'C' and resid 821 through 825
Processing helix chain 'C' and resid 859 through 864
removed outlier: 4.758A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A)
Processing helix chain 'C' and resid 897 through 906
removed outlier: 3.864A pdb=" N ILE C 905 " --> pdb=" O LEU C 901 " (cutoff:3.500A)
removed outlier: 3.569A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A)
Processing helix chain 'C' and resid 944 through 980
removed outlier: 4.495A pdb=" N ALA C 969 " --> pdb=" O GLN C 965 " (cutoff:3.500A)
removed outlier: 4.170A pdb=" N SER C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A)
removed outlier: 4.724A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A)
removed outlier: 4.194A pdb=" N ILE C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A)
removed outlier: 5.028A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A)
removed outlier: 4.143A pdb=" N VAL C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A)
Processing helix chain 'C' and resid 995 through 997
No H-bonds generated for 'chain 'C' and resid 995 through 997'
Processing helix chain 'C' and resid 1009 through 1037
removed outlier: 3.741A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A)
Processing helix chain 'C' and resid 1100 through 1106
Proline residue: C1104 - end of helix
Processing helix chain 'C' and resid 1109 through 1133
removed outlier: 4.187A pdb=" N LYS C1122 " --> pdb=" O MET C1119 " (cutoff:3.500A)
removed outlier: 4.108A pdb=" N LYS C1133 " --> pdb=" O ALA C1130 " (cutoff:3.500A)
Processing helix chain 'C' and resid 1138 through 1149
Processing helix chain 'C' and resid 1167 through 1176
Processing helix chain 'C' and resid 1192 through 1202
Processing helix chain 'C' and resid 1239 through 1241
No H-bonds generated for 'chain 'C' and resid 1239 through 1241'
Processing helix chain 'C' and resid 1262 through 1264
No H-bonds generated for 'chain 'C' and resid 1262 through 1264'
Processing helix chain 'C' and resid 1272 through 1281
removed outlier: 3.824A pdb=" N LEU C1278 " --> pdb=" O GLU C1274 " (cutoff:3.500A)
Processing helix chain 'C' and resid 1284 through 1292
Processing helix chain 'C' and resid 1298 through 1309
Processing helix chain 'C' and resid 1321 through 1333
Processing helix chain 'D' and resid 27 through 33
Processing helix chain 'D' and resid 59 through 62
No H-bonds generated for 'chain 'D' and resid 59 through 62'
Processing helix chain 'D' and resid 125 through 128
No H-bonds generated for 'chain 'D' and resid 125 through 128'
Processing helix chain 'D' and resid 132 through 139
Processing helix chain 'D' and resid 165 through 172
removed outlier: 3.517A pdb=" N PHE D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A)
Processing helix chain 'D' and resid 182 through 191
removed outlier: 4.203A pdb=" N GLN D 186 " --> pdb=" O GLU D 183 " (cutoff:3.500A)
removed outlier: 4.534A pdb=" N ALA D 187 " --> pdb=" O ALA D 184 " (cutoff:3.500A)
Processing helix chain 'D' and resid 194 through 207
removed outlier: 3.758A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A)
Processing helix chain 'D' and resid 211 through 230
Processing helix chain 'D' and resid 235 through 237
No H-bonds generated for 'chain 'D' and resid 235 through 237'
Processing helix chain 'D' and resid 247 through 249
No H-bonds generated for 'chain 'D' and resid 247 through 249'
Processing helix chain 'D' and resid 265 through 283
removed outlier: 4.172A pdb=" N TYR D 269 " --> pdb=" O ASN D 266 " (cutoff:3.500A)
removed outlier: 4.089A pdb=" N ARG D 281 " --> pdb=" O ARG D 278 " (cutoff:3.500A)
Processing helix chain 'D' and resid 289 through 307
Processing helix chain 'D' and resid 328 through 331
Processing helix chain 'D' and resid 337 through 340
No H-bonds generated for 'chain 'D' and resid 337 through 340'
Processing helix chain 'D' and resid 370 through 388
removed outlier: 3.780A pdb=" N LYS D 378 " --> pdb=" O LEU D 374 " (cutoff:3.500A)
Proline residue: D 379 - end of helix
Processing helix chain 'D' and resid 394 through 403
Processing helix chain 'D' and resid 406 through 416
Processing helix chain 'D' and resid 431 through 433
No H-bonds generated for 'chain 'D' and resid 431 through 433'
Processing helix chain 'D' and resid 451 through 457
Processing helix chain 'D' and resid 474 through 482
Processing helix chain 'D' and resid 486 through 488
No H-bonds generated for 'chain 'D' and resid 486 through 488'
Processing helix chain 'D' and resid 506 through 513
Processing helix chain 'D' and resid 530 through 539
Processing helix chain 'D' and resid 574 through 582
removed outlier: 3.838A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A)
removed outlier: 4.356A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A)
Processing helix chain 'D' and resid 590 through 592
No H-bonds generated for 'chain 'D' and resid 590 through 592'
Processing helix chain 'D' and resid 598 through 611
Processing helix chain 'D' and resid 614 through 635
Processing helix chain 'D' and resid 651 through 670
removed outlier: 4.088A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A)
Processing helix chain 'D' and resid 675 through 701
Processing helix chain 'D' and resid 723 through 727
Processing helix chain 'D' and resid 734 through 741
Processing helix chain 'D' and resid 769 through 787
removed outlier: 4.684A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A)
removed outlier: 4.779A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A)
removed outlier: 3.936A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A)
Processing helix chain 'D' and resid 790 through 804
Processing helix chain 'D' and resid 835 through 839
Processing helix chain 'D' and resid 866 through 874
Processing helix chain 'D' and resid 916 through 929
removed outlier: 3.547A pdb=" N GLU D 925 " --> pdb=" O GLN D 921 " (cutoff:3.500A)
Proline residue: D 926 - end of helix
removed outlier: 4.490A pdb=" N GLN D 929 " --> pdb=" O GLU D 925 " (cutoff:3.500A)
Processing helix chain 'D' and resid 1138 through 1145
Processing helix chain 'D' and resid 1218 through 1221
No H-bonds generated for 'chain 'D' and resid 1218 through 1221'
Processing helix chain 'D' and resid 1227 through 1244
removed outlier: 4.127A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A)
Processing helix chain 'D' and resid 1251 through 1260
removed outlier: 4.161A pdb=" N ILE D1256 " --> pdb=" O ILE D1253 " (cutoff:3.500A)
Processing helix chain 'D' and resid 1280 through 1287
Processing helix chain 'D' and resid 1309 through 1314
Processing helix chain 'D' and resid 1328 through 1337
Processing helix chain 'D' and resid 1347 through 1351
Processing helix chain 'D' and resid 1363 through 1374
Processing helix chain 'E' and resid 7 through 13
removed outlier: 3.567A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A)
Processing helix chain 'E' and resid 16 through 26
Processing helix chain 'E' and resid 28 through 31
No H-bonds generated for 'chain 'E' and resid 28 through 31'
Processing helix chain 'E' and resid 46 through 55
Processing helix chain 'E' and resid 61 through 79
Processing helix chain 'F' and resid 97 through 106
Processing helix chain 'F' and resid 115 through 135
Processing helix chain 'F' and resid 145 through 152
Processing helix chain 'F' and resid 160 through 164
Processing helix chain 'F' and resid 214 through 221
removed outlier: 3.526A pdb=" N PHE F 221 " --> pdb=" O ALA F 217 " (cutoff:3.500A)
Processing helix chain 'F' and resid 223 through 232
Processing helix chain 'F' and resid 243 through 257
Processing helix chain 'F' and resid 264 through 292
removed outlier: 3.637A pdb=" N TYR F 268 " --> pdb=" O GLN F 265 " (cutoff:3.500A)
removed outlier: 3.674A pdb=" N SER F 272 " --> pdb=" O LEU F 269 " (cutoff:3.500A)
removed outlier: 4.204A pdb=" N VAL F 275 " --> pdb=" O SER F 272 " (cutoff:3.500A)
removed outlier: 4.044A pdb=" N MET F 276 " --> pdb=" O MET F 273 " (cutoff:3.500A)
removed outlier: 3.503A pdb=" N MET F 277 " --> pdb=" O ARG F 274 " (cutoff:3.500A)
removed outlier: 4.702A pdb=" N ARG F 281 " --> pdb=" O ASP F 278 " (cutoff:3.500A)
removed outlier: 4.216A pdb=" N GLU F 284 " --> pdb=" O ARG F 281 " (cutoff:3.500A)
removed outlier: 4.011A pdb=" N MET F 288 " --> pdb=" O ARG F 285 " (cutoff:3.500A)
removed outlier: 4.408A pdb=" N VAL F 292 " --> pdb=" O LYS F 289 " (cutoff:3.500A)
Processing helix chain 'F' and resid 300 through 305
Processing helix chain 'F' and resid 314 through 319
Processing helix chain 'F' and resid 334 through 343
removed outlier: 3.725A pdb=" N HIS F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A)
removed outlier: 3.757A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A)
Processing helix chain 'F' and resid 345 through 351
Processing helix chain 'F' and resid 356 through 375
removed outlier: 3.599A pdb=" N ARG F 363 " --> pdb=" O LYS F 359 " (cutoff:3.500A)
removed outlier: 4.168A pdb=" N ALA F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A)
Processing helix chain 'F' and resid 377 through 382
Processing helix chain 'F' and resid 384 through 394
removed outlier: 3.831A pdb=" N LYS F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A)
removed outlier: 3.960A pdb=" N TYR F 394 " --> pdb=" O ILE F 390 " (cutoff:3.500A)
Processing helix chain 'F' and resid 401 through 417
Processing helix chain 'F' and resid 427 through 445
removed outlier: 3.814A pdb=" N ALA F 444 " --> pdb=" O THR F 440 " (cutoff:3.500A)
Processing helix chain 'F' and resid 454 through 474
removed outlier: 3.705A pdb=" N ARG F 468 " --> pdb=" O ASN F 464 " (cutoff:3.500A)
Processing helix chain 'F' and resid 480 through 487
Processing helix chain 'F' and resid 491 through 498
Processing helix chain 'F' and resid 519 through 521
No H-bonds generated for 'chain 'F' and resid 519 through 521'
Processing helix chain 'F' and resid 531 through 550
removed outlier: 3.769A pdb=" N GLY F 550 " --> pdb=" O ASP F 546 " (cutoff:3.500A)
Processing helix chain 'F' and resid 553 through 561
Processing helix chain 'F' and resid 573 through 579
removed outlier: 3.861A pdb=" N GLY F 577 " --> pdb=" O LEU F 573 " (cutoff:3.500A)
Processing helix chain 'F' and resid 585 through 599
Processing helix chain 'G' and resid 10 through 17
removed outlier: 3.944A pdb=" N HIS G 17 " --> pdb=" O TRP G 13 " (cutoff:3.500A)
Processing helix chain 'G' and resid 72 through 74
No H-bonds generated for 'chain 'G' and resid 72 through 74'
Processing helix chain 'G' and resid 101 through 108
Processing helix chain 'G' and resid 112 through 136
Processing helix chain 'G' and resid 139 through 151
removed outlier: 3.595A pdb=" N ALA G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A)
Processing helix chain 'G' and resid 171 through 176
Processing helix chain 'G' and resid 180 through 190
Processing helix chain 'H' and resid 10 through 17
removed outlier: 4.419A pdb=" N HIS H 17 " --> pdb=" O TRP H 13 " (cutoff:3.500A)
Processing helix chain 'H' and resid 99 through 108
removed outlier: 3.778A pdb=" N GLN H 104 " --> pdb=" O LYS H 100 " (cutoff:3.500A)
Processing helix chain 'H' and resid 114 through 136
Processing helix chain 'H' and resid 139 through 150
Processing helix chain 'H' and resid 169 through 175
removed outlier: 3.829A pdb=" N GLN H 174 " --> pdb=" O GLN H 170 " (cutoff:3.500A)
Processing helix chain 'H' and resid 180 through 191
Processing sheet with id= A, first strand: chain 'A' and resid 24 through 28
Processing sheet with id= B, first strand: chain 'A' and resid 90 through 92
Processing sheet with id= C, first strand: chain 'A' and resid 97 through 105
removed outlier: 5.719A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A)
removed outlier: 5.616A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A)
removed outlier: 7.391A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A)
removed outlier: 5.208A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A)
Processing sheet with id= D, first strand: chain 'A' and resid 108 through 110
Processing sheet with id= E, first strand: chain 'B' and resid 24 through 26
removed outlier: 4.371A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A)
Processing sheet with id= F, first strand: chain 'B' and resid 52 through 56
Processing sheet with id= G, first strand: chain 'B' and resid 59 through 61
Processing sheet with id= H, first strand: chain 'B' and resid 12 through 15
removed outlier: 3.592A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A)
removed outlier: 3.572A pdb=" N VAL B 14 " --> pdb=" O THR B 27 " (cutoff:3.500A)
removed outlier: 6.607A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A)
Processing sheet with id= I, first strand: chain 'B' and resid 109 through 111
removed outlier: 3.714A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A)
Processing sheet with id= J, first strand: chain 'C' and resid 117 through 123
removed outlier: 3.606A pdb=" N LYS C 118 " --> pdb=" O LEU C 102 " (cutoff:3.500A)
removed outlier: 3.781A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A)
removed outlier: 5.411A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A)
removed outlier: 5.279A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A)
Processing sheet with id= K, first strand: chain 'C' and resid 148 through 151
Processing sheet with id= L, first strand: chain 'C' and resid 154 through 161
removed outlier: 6.285A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A)
Processing sheet with id= M, first strand: chain 'C' and resid 228 through 230
Processing sheet with id= N, first strand: chain 'C' and resid 231 through 233
Processing sheet with id= O, first strand: chain 'C' and resid 579 through 581
Processing sheet with id= P, first strand: chain 'C' and resid 634 through 638
Processing sheet with id= Q, first strand: chain 'C' and resid 750 through 752
removed outlier: 5.661A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A)
removed outlier: 5.470A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A)
Processing sheet with id= R, first strand: chain 'C' and resid 798 through 803
Processing sheet with id= S, first strand: chain 'C' and resid 816 through 818
Processing sheet with id= T, first strand: chain 'C' and resid 830 through 832
Processing sheet with id= U, first strand: chain 'C' and resid 876 through 878
removed outlier: 3.851A pdb=" N ILE C 929 " --> pdb=" O TYR C1053 " (cutoff:3.500A)
removed outlier: 7.448A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A)
removed outlier: 4.880A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A)
removed outlier: 6.803A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A)
removed outlier: 4.478A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A)
removed outlier: 6.546A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A)
removed outlier: 5.607A pdb=" N THR C 935 " --> pdb=" O LEU C1047 " (cutoff:3.500A)
removed outlier: 8.564A pdb=" N LEU C1047 " --> pdb=" O THR C 935 " (cutoff:3.500A)
removed outlier: 6.777A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A)
removed outlier: 4.866A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A)
removed outlier: 6.922A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A)
removed outlier: 4.718A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A)
removed outlier: 6.911A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A)
Processing sheet with id= V, first strand: chain 'C' and resid 887 through 889
Processing sheet with id= W, first strand: chain 'D' and resid 103 through 106
Processing sheet with id= X, first strand: chain 'D' and resid 143 through 145
Processing sheet with id= Y, first strand: chain 'D' and resid 252 through 254
Processing sheet with id= Z, first strand: chain 'D' and resid 350 through 354
Processing sheet with id= AA, first strand: chain 'D' and resid 548 through 552
Processing sheet with id= AB, first strand: chain 'D' and resid 820 through 822
Processing sheet with id= AC, first strand: chain 'D' and resid 965 through 967
Processing sheet with id= AD, first strand: chain 'D' and resid 1034 through 1036
removed outlier: 3.977A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A)
removed outlier: 4.100A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A)
Processing sheet with id= AE, first strand: chain 'D' and resid 1162 through 1165
Processing sheet with id= AF, first strand: chain 'D' and resid 950 through 952
removed outlier: 6.629A pdb=" N VAL D 952 " --> pdb=" O THR D1016 " (cutoff:3.500A)
removed outlier: 5.773A pdb=" N THR D1016 " --> pdb=" O VAL D 952 " (cutoff:3.500A)
Processing sheet with id= AG, first strand: chain 'D' and resid 981 through 985
Processing sheet with id= AH, first strand: chain 'G' and resid 19 through 23
removed outlier: 5.819A pdb=" N ALA G 95 " --> pdb=" O ILE G 42 " (cutoff:3.500A)
removed outlier: 5.622A pdb=" N ILE G 42 " --> pdb=" O ALA G 95 " (cutoff:3.500A)
removed outlier: 7.011A pdb=" N ILE G 97 " --> pdb=" O TYR G 40 " (cutoff:3.500A)
removed outlier: 4.955A pdb=" N TYR G 40 " --> pdb=" O ILE G 97 " (cutoff:3.500A)
Processing sheet with id= AI, first strand: chain 'G' and resid 48 through 50
Processing sheet with id= AJ, first strand: chain 'H' and resid 21 through 23
removed outlier: 6.420A pdb=" N ALA H 95 " --> pdb=" O ILE H 42 " (cutoff:3.500A)
removed outlier: 5.787A pdb=" N ILE H 42 " --> pdb=" O ALA H 95 " (cutoff:3.500A)
removed outlier: 6.547A pdb=" N ILE H 97 " --> pdb=" O TYR H 40 " (cutoff:3.500A)
removed outlier: 4.941A pdb=" N TYR H 40 " --> pdb=" O ILE H 97 " (cutoff:3.500A)
Processing sheet with id= AK, first strand: chain 'H' and resid 85 through 87
removed outlier: 6.599A pdb=" N ILE H 51 " --> pdb=" O ILE H 60 " (cutoff:3.500A)
removed outlier: 5.154A pdb=" N ILE H 60 " --> pdb=" O ILE H 51 " (cutoff:3.500A)
Processing sheet with id= AL, first strand: chain 'H' and resid 163 through 165
1070 hydrogen bonds defined for protein.
2868 hydrogen bond angles defined for protein.
Restraints generated for nucleic acids:
106 hydrogen bonds
212 hydrogen bond angles
0 basepair planarities
45 basepair parallelities
112 stacking parallelities
Total time for adding SS restraints: 26.34
Time building geometry restraints manager: 50.38 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
0.83 - 1.03: 34377
1.03 - 1.23: 302
1.23 - 1.43: 14734
1.43 - 1.63: 21123
1.63 - 1.83: 259
Bond restraints: 70795
Sorted by residual:
bond pdb=" C ASP F 167 "
pdb=" O ASP F 167 "
ideal model delta sigma weight residual
1.233 1.254 -0.021 4.80e-03 4.34e+04 1.93e+01
bond pdb=" CB ILE C 833 "
pdb=" HB ILE C 833 "
ideal model delta sigma weight residual
0.970 0.901 0.069 2.00e-02 2.50e+03 1.18e+01
bond pdb=" C3' DT 1 47 "
pdb=" O3' DT 1 47 "
ideal model delta sigma weight residual
1.422 1.519 -0.097 3.00e-02 1.11e+03 1.04e+01
bond pdb=" C PRO C 375 "
pdb=" N PRO C 376 "
ideal model delta sigma weight residual
1.334 1.408 -0.074 2.34e-02 1.83e+03 9.98e+00
bond pdb=" C3' DG 2 42 "
pdb=" O3' DG 2 42 "
ideal model delta sigma weight residual
1.422 1.509 -0.087 3.00e-02 1.11e+03 8.38e+00
... (remaining 70790 not shown)
Histogram of bond angle deviations from ideal:
95.55 - 103.78: 878
103.78 - 112.00: 80975
112.00 - 120.23: 25603
120.23 - 128.46: 20557
128.46 - 136.69: 402
Bond angle restraints: 128415
Sorted by residual:
angle pdb=" C3' DC 2 41 "
pdb=" O3' DC 2 41 "
pdb=" P DG 2 42 "
ideal model delta sigma weight residual
120.20 127.47 -7.27 1.50e+00 4.44e-01 2.35e+01
angle pdb=" N GLY C 627 "
pdb=" CA GLY C 627 "
pdb=" C GLY C 627 "
ideal model delta sigma weight residual
110.21 105.88 4.33 9.10e-01 1.21e+00 2.27e+01
angle pdb=" O3' DC 2 41 "
pdb=" C3' DC 2 41 "
pdb=" C2' DC 2 41 "
ideal model delta sigma weight residual
111.50 118.41 -6.91 1.50e+00 4.44e-01 2.12e+01
angle pdb=" N VAL C 663 "
pdb=" CA VAL C 663 "
pdb=" C VAL C 663 "
ideal model delta sigma weight residual
110.74 114.84 -4.10 9.10e-01 1.21e+00 2.03e+01
angle pdb=" C VAL D 407 "
pdb=" N VAL D 408 "
pdb=" CA VAL D 408 "
ideal model delta sigma weight residual
120.60 126.25 -5.65 1.29e+00 6.01e-01 1.92e+01
... (remaining 128410 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 35.99: 26606
35.99 - 71.98: 955
71.98 - 107.98: 33
107.98 - 143.97: 5
143.97 - 179.96: 10
Dihedral angle restraints: 27609
sinusoidal: 14516
harmonic: 13093
Sorted by residual:
dihedral pdb=" CA LEU D 120 "
pdb=" C LEU D 120 "
pdb=" N PRO D 121 "
pdb=" CA PRO D 121 "
ideal model delta harmonic sigma weight residual
-180.00 -116.23 -63.77 0 5.00e+00 4.00e-02 1.63e+02
dihedral pdb=" CA PHE F 165 "
pdb=" C PHE F 165 "
pdb=" N VAL F 166 "
pdb=" CA VAL F 166 "
ideal model delta harmonic sigma weight residual
180.00 -119.42 -60.58 0 5.00e+00 4.00e-02 1.47e+02
dihedral pdb=" CA GLN F 294 "
pdb=" C GLN F 294 "
pdb=" N CYS F 295 "
pdb=" CA CYS F 295 "
ideal model delta harmonic sigma weight residual
-180.00 -130.50 -49.50 0 5.00e+00 4.00e-02 9.80e+01
... (remaining 27606 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.086: 4899
0.086 - 0.172: 735
0.172 - 0.257: 33
0.257 - 0.343: 1
0.343 - 0.429: 1
Chirality restraints: 5669
Sorted by residual:
chirality pdb=" CB ILE C 833 "
pdb=" CA ILE C 833 "
pdb=" CG1 ILE C 833 "
pdb=" CG2 ILE C 833 "
both_signs ideal model delta sigma weight residual
False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.60e+00
chirality pdb=" CB ILE F 452 "
pdb=" CA ILE F 452 "
pdb=" CG1 ILE F 452 "
pdb=" CG2 ILE F 452 "
both_signs ideal model delta sigma weight residual
False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.67e+00
chirality pdb=" CB VAL C 724 "
pdb=" CA VAL C 724 "
pdb=" CG1 VAL C 724 "
pdb=" CG2 VAL C 724 "
both_signs ideal model delta sigma weight residual
False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.54e+00
... (remaining 5666 not shown)
Planarity restraints: 9956
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C LEU D 120 " 0.060 5.00e-02 4.00e+02 9.12e-02 1.33e+01
pdb=" N PRO D 121 " -0.158 5.00e-02 4.00e+02
pdb=" CA PRO D 121 " 0.048 5.00e-02 4.00e+02
pdb=" CD PRO D 121 " 0.049 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" C1' DC 1 80 " 0.045 2.00e-02 2.50e+03 2.07e-02 1.18e+01
pdb=" N1 DC 1 80 " -0.048 2.00e-02 2.50e+03
pdb=" C2 DC 1 80 " 0.002 2.00e-02 2.50e+03
pdb=" O2 DC 1 80 " -0.012 2.00e-02 2.50e+03
pdb=" N3 DC 1 80 " 0.005 2.00e-02 2.50e+03
pdb=" C4 DC 1 80 " 0.007 2.00e-02 2.50e+03
pdb=" N4 DC 1 80 " 0.009 2.00e-02 2.50e+03
pdb=" C5 DC 1 80 " 0.002 2.00e-02 2.50e+03
pdb=" C6 DC 1 80 " 0.001 2.00e-02 2.50e+03
pdb=" H5 DC 1 80 " -0.001 2.00e-02 2.50e+03
pdb=" H6 DC 1 80 " -0.011 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C1' DT 1 47 " 0.046 2.00e-02 2.50e+03 1.96e-02 1.15e+01
pdb=" N1 DT 1 47 " -0.043 2.00e-02 2.50e+03
pdb=" C2 DT 1 47 " -0.001 2.00e-02 2.50e+03
pdb=" O2 DT 1 47 " -0.019 2.00e-02 2.50e+03
pdb=" N3 DT 1 47 " 0.006 2.00e-02 2.50e+03
pdb=" C4 DT 1 47 " 0.006 2.00e-02 2.50e+03
pdb=" O4 DT 1 47 " 0.007 2.00e-02 2.50e+03
pdb=" C5 DT 1 47 " 0.002 2.00e-02 2.50e+03
pdb=" C7 DT 1 47 " -0.003 2.00e-02 2.50e+03
pdb=" C6 DT 1 47 " -0.006 2.00e-02 2.50e+03
pdb=" H3 DT 1 47 " 0.010 2.00e-02 2.50e+03
pdb=" H6 DT 1 47 " -0.005 2.00e-02 2.50e+03
... (remaining 9953 not shown)
Histogram of nonbonded interaction distances:
1.10 - 1.80: 261
1.80 - 2.50: 56934
2.50 - 3.20: 221091
3.20 - 3.90: 274016
3.90 - 4.60: 430501
Nonbonded interactions: 982803
Sorted by model distance:
nonbonded pdb=" OD1 ASP D 464 "
pdb="HO2' G 3 3 "
model vdw
1.096 1.850
nonbonded pdb=" O GLU D1334 "
pdb=" HZ3 LYS D1340 "
model vdw
1.561 1.850
nonbonded pdb="HH11 ARG D 905 "
pdb=" O ILE D 908 "
model vdw
1.565 1.850
nonbonded pdb=" O ASN D 274 "
pdb=" H ARG D 278 "
model vdw
1.578 1.850
nonbonded pdb=" O GLN D 186 "
pdb=" H LYS D 190 "
model vdw
1.588 1.850
... (remaining 982798 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 6 through 233)
selection = chain 'B'
}
ncs_group {
reference = chain 'G'
selection = chain 'H'
}
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: 8
Type Number sf(0) Gaussians
Zn 2 6.06 5
P 163 5.49 5
Mg 1 5.21 5
S 147 5.16 5
C 21765 2.51 5
N 6293 2.21 5
O 7142 1.98 5
H 34409 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 2.870
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: 0.770
Extract box with map and model: 15.470
Check model and map are aligned: 0.780
Process input model: 207.780
Find NCS groups from input model: 1.370
Set up NCS constraints: 0.190
Set refine NCS operators: 0.000
Set scattering table: 0.460
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.010
Load rotamer database and sin/cos tables:2.670
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 232.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3905
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 : 0.010 0.115 36386 Z= 0.647
Angle : 1.164 10.216 49818 Z= 0.658
Chirality : 0.058 0.429 5669
Planarity : 0.007 0.091 5925
Dihedral : 16.288 179.873 14202
Min Nonbonded Distance : 1.840
Molprobity Statistics.
All-atom Clashscore : 11.04
Ramachandran Plot:
Outliers : 0.42 %
Allowed : 11.45 %
Favored : 88.13 %
Rotamer Outliers : 0.06 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 1.95 %
Twisted General : 1.07 %
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: -4.77 (0.10), residues: 4069
helix: -3.14 (0.09), residues: 1468
sheet: -3.20 (0.22), residues: 406
loop : -3.23 (0.11), residues: 2195
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
516 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 2
poor density : 514
time to evaluate : 4.185
Fit side-chains
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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
outliers start: 2
outliers final: 1
residues processed: 516
average time/residue: 1.0776
time to fit residues: 852.6748
Evaluate side-chains
357 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 356
time to evaluate : 4.297
Switching outliers to nearest non-outliers
revert: symmetry clash
outliers start: 1
outliers final: 1
residues processed: 1
average time/residue: 0.6306
time to fit residues: 6.5509
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 419
random chunks:
chunk 353 optimal weight: 10.0000
chunk 317 optimal weight: 5.9990
chunk 176 optimal weight: 10.0000
chunk 108 optimal weight: 0.9990
chunk 214 optimal weight: 0.9980
chunk 169 optimal weight: 6.9990
chunk 328 optimal weight: 10.0000
chunk 127 optimal weight: 3.9990
chunk 199 optimal weight: 3.9990
chunk 244 optimal weight: 9.9990
chunk 380 optimal weight: 8.9990
overall best weight: 3.1988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
C 165 HIS
** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1257 GLN
D1197 ASN
D1279 GLN
** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 159 HIS
H 65 ASN
H 194 ASN
Total number of N/Q/H flips: 7
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3838
moved from start: 0.1874
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.066 36386 Z= 0.245
Angle : 0.744 8.791 49818 Z= 0.414
Chirality : 0.043 0.237 5669
Planarity : 0.006 0.116 5925
Dihedral : 19.840 178.097 6091
Min Nonbonded Distance : 1.913
Molprobity Statistics.
All-atom Clashscore : 16.11
Ramachandran Plot:
Outliers : 0.32 %
Allowed : 9.93 %
Favored : 89.75 %
Rotamer Outliers : 0.03 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 1.30 %
Twisted General : 0.38 %
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: -3.96 (0.11), residues: 4069
helix: -2.30 (0.11), residues: 1494
sheet: -2.82 (0.22), residues: 418
loop : -2.87 (0.12), residues: 2157
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
452 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 451
time to evaluate : 4.099
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
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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
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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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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: 452
average time/residue: 1.1093
time to fit residues: 763.2331
Evaluate side-chains
361 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 360
time to evaluate : 4.124
Switching outliers to nearest non-outliers
outliers start: 1
outliers final: 0
residues processed: 1
average time/residue: 0.6098
time to fit residues: 6.3047
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 419
random chunks:
chunk 211 optimal weight: 8.9990
chunk 118 optimal weight: 1.9990
chunk 316 optimal weight: 20.0000
chunk 259 optimal weight: 0.9990
chunk 104 optimal weight: 0.7980
chunk 381 optimal weight: 9.9990
chunk 411 optimal weight: 10.0000
chunk 339 optimal weight: 9.9990
chunk 378 optimal weight: 20.0000
chunk 129 optimal weight: 0.3980
chunk 305 optimal weight: 9.9990
overall best weight: 2.6386
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 194 GLN
** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 767 GLN
D 266 ASN
D1197 ASN
** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 31 HIS
G 159 HIS
** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3817
moved from start: 0.2568
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.065 36386 Z= 0.215
Angle : 0.675 9.072 49818 Z= 0.374
Chirality : 0.042 0.188 5669
Planarity : 0.005 0.075 5925
Dihedral : 19.593 177.360 6091
Min Nonbonded Distance : 1.860
Molprobity Statistics.
All-atom Clashscore : 15.24
Ramachandran Plot:
Outliers : 0.22 %
Allowed : 9.46 %
Favored : 90.32 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 1.30 %
Twisted General : 0.23 %
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: -3.45 (0.12), residues: 4069
helix: -1.72 (0.12), residues: 1506
sheet: -2.61 (0.22), residues: 442
loop : -2.68 (0.12), residues: 2121
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
438 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 438
time to evaluate : 4.126
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
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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
revert: symmetry clash
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
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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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: 438
average time/residue: 1.0662
time to fit residues: 710.8939
Evaluate side-chains
360 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 360
time to evaluate : 4.135
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 5.1558
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 419
random chunks:
chunk 376 optimal weight: 5.9990
chunk 286 optimal weight: 20.0000
chunk 197 optimal weight: 8.9990
chunk 42 optimal weight: 20.0000
chunk 181 optimal weight: 6.9990
chunk 255 optimal weight: 10.0000
chunk 382 optimal weight: 0.7980
chunk 405 optimal weight: 20.0000
chunk 199 optimal weight: 5.9990
chunk 362 optimal weight: 10.0000
chunk 109 optimal weight: 8.9990
overall best weight: 5.7588
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN
C 580 GLN
** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1197 ASN
E 31 GLN
** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 31 HIS
G 159 HIS
H 174 GLN
Total number of N/Q/H flips: 7
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3964
moved from start: 0.3101
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.005 0.079 36386 Z= 0.297
Angle : 0.714 9.291 49818 Z= 0.397
Chirality : 0.043 0.173 5669
Planarity : 0.005 0.074 5925
Dihedral : 19.609 179.138 6091
Min Nonbonded Distance : 1.735
Molprobity Statistics.
All-atom Clashscore : 20.88
Ramachandran Plot:
Outliers : 0.22 %
Allowed : 11.16 %
Favored : 88.62 %
Rotamer Outliers : 0.03 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 0.65 %
Twisted General : 0.20 %
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: -3.46 (0.11), residues: 4069
helix: -1.60 (0.12), residues: 1488
sheet: -2.71 (0.21), residues: 476
loop : -2.75 (0.12), residues: 2105
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
403 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 402
time to evaluate : 4.260
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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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: 403
average time/residue: 1.0463
time to fit residues: 640.8950
Evaluate side-chains
341 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 340
time to evaluate : 4.555
Switching outliers to nearest non-outliers
outliers start: 1
outliers final: 0
residues processed: 1
average time/residue: 0.5922
time to fit residues: 6.2904
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 419
random chunks:
chunk 337 optimal weight: 0.9980
chunk 229 optimal weight: 3.9990
chunk 5 optimal weight: 9.9990
chunk 301 optimal weight: 10.0000
chunk 167 optimal weight: 8.9990
chunk 345 optimal weight: 9.9990
chunk 279 optimal weight: 30.0000
chunk 0 optimal weight: 10.0000
chunk 206 optimal weight: 8.9990
chunk 363 optimal weight: 5.9990
chunk 102 optimal weight: 10.0000
overall best weight: 5.7988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1257 GLN
D 954 ASN
D1197 ASN
** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 31 HIS
G 80 GLN
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4001
moved from start: 0.3599
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.065 36386 Z= 0.280
Angle : 0.692 9.717 49818 Z= 0.386
Chirality : 0.042 0.174 5669
Planarity : 0.005 0.071 5925
Dihedral : 19.615 179.393 6091
Min Nonbonded Distance : 1.808
Molprobity Statistics.
All-atom Clashscore : 20.88
Ramachandran Plot:
Outliers : 0.22 %
Allowed : 11.06 %
Favored : 88.72 %
Rotamer Outliers : 0.03 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 0.65 %
Twisted General : 0.20 %
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: -3.38 (0.12), residues: 4069
helix: -1.58 (0.12), residues: 1500
sheet: -2.64 (0.21), residues: 483
loop : -2.67 (0.12), residues: 2086
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
407 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 406
time to evaluate : 4.121
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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 1
outliers final: 0
residues processed: 407
average time/residue: 1.0529
time to fit residues: 653.8572
Evaluate side-chains
346 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 346
time to evaluate : 4.146
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 5.1734
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 419
random chunks:
chunk 136 optimal weight: 5.9990
chunk 364 optimal weight: 0.1980
chunk 80 optimal weight: 9.9990
chunk 237 optimal weight: 1.9990
chunk 99 optimal weight: 10.0000
chunk 405 optimal weight: 10.0000
chunk 336 optimal weight: 30.0000
chunk 187 optimal weight: 0.0980
chunk 33 optimal weight: 9.9990
chunk 134 optimal weight: 10.0000
chunk 212 optimal weight: 8.9990
overall best weight: 3.4586
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 686 GLN
** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1197 ASN
D1218 HIS
** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 31 HIS
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3951
moved from start: 0.3909
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.062 36386 Z= 0.215
Angle : 0.633 9.514 49818 Z= 0.353
Chirality : 0.041 0.171 5669
Planarity : 0.005 0.072 5925
Dihedral : 19.512 179.032 6091
Min Nonbonded Distance : 1.834
Molprobity Statistics.
All-atom Clashscore : 17.37
Ramachandran Plot:
Outliers : 0.17 %
Allowed : 10.25 %
Favored : 89.58 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 0.65 %
Twisted General : 0.20 %
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: -3.08 (0.12), residues: 4069
helix: -1.26 (0.12), residues: 1505
sheet: -2.55 (0.21), residues: 480
loop : -2.53 (0.12), residues: 2084
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
406 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 406
time to evaluate : 4.192
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
revert: symmetry clash
outliers start: 0
outliers final: 0
residues processed: 406
average time/residue: 1.0777
time to fit residues: 667.1526
Evaluate side-chains
346 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 346
time to evaluate : 4.152
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 5.1430
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 419
random chunks:
chunk 390 optimal weight: 6.9990
chunk 45 optimal weight: 10.0000
chunk 230 optimal weight: 10.0000
chunk 296 optimal weight: 10.0000
chunk 229 optimal weight: 10.0000
chunk 341 optimal weight: 3.9990
chunk 226 optimal weight: 10.0000
chunk 403 optimal weight: 9.9990
chunk 252 optimal weight: 8.9990
chunk 246 optimal weight: 8.9990
chunk 186 optimal weight: 9.9990
overall best weight: 7.7990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 659 GLN
** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 760 ASN
C1257 GLN
** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1252 HIS
** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 31 HIS
** G 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4134
moved from start: 0.4431
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.006 0.075 36386 Z= 0.374
Angle : 0.757 9.622 49818 Z= 0.423
Chirality : 0.044 0.248 5669
Planarity : 0.006 0.158 5925
Dihedral : 19.667 178.885 6091
Min Nonbonded Distance : 1.704
Molprobity Statistics.
All-atom Clashscore : 29.75
Ramachandran Plot:
Outliers : 0.22 %
Allowed : 13.22 %
Favored : 86.56 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 0.65 %
Twisted General : 0.20 %
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: -3.50 (0.12), residues: 4069
helix: -1.65 (0.12), residues: 1481
sheet: -2.69 (0.21), residues: 477
loop : -2.78 (0.12), residues: 2111
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
385 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 385
time to evaluate : 4.135
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
revert: symmetry clash
outliers start: 0
outliers final: 0
residues processed: 385
average time/residue: 1.0701
time to fit residues: 627.8535
Evaluate side-chains
331 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 331
time to evaluate : 4.121
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 5.1135
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 419
random chunks:
chunk 249 optimal weight: 10.0000
chunk 161 optimal weight: 6.9990
chunk 241 optimal weight: 8.9990
chunk 121 optimal weight: 6.9990
chunk 79 optimal weight: 9.9990
chunk 78 optimal weight: 6.9990
chunk 256 optimal weight: 10.0000
chunk 275 optimal weight: 9.9990
chunk 199 optimal weight: 4.9990
chunk 37 optimal weight: 8.9990
chunk 317 optimal weight: 20.0000
overall best weight: 6.9990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4121
moved from start: 0.4828
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.005 0.074 36386 Z= 0.312
Angle : 0.708 9.661 49818 Z= 0.396
Chirality : 0.043 0.183 5669
Planarity : 0.006 0.078 5925
Dihedral : 19.695 178.654 6091
Min Nonbonded Distance : 1.777
Molprobity Statistics.
All-atom Clashscore : 25.92
Ramachandran Plot:
Outliers : 0.20 %
Allowed : 11.99 %
Favored : 87.81 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 0.65 %
Twisted General : 0.15 %
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: -3.41 (0.12), residues: 4069
helix: -1.55 (0.12), residues: 1477
sheet: -2.62 (0.21), residues: 462
loop : -2.74 (0.12), residues: 2130
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
378 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 378
time to evaluate : 4.181
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
outliers start: 0
outliers final: 0
residues processed: 378
average time/residue: 1.0724
time to fit residues: 614.9724
Evaluate side-chains
318 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 318
time to evaluate : 4.193
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 5.1650
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 419
random chunks:
chunk 367 optimal weight: 20.0000
chunk 386 optimal weight: 10.0000
chunk 352 optimal weight: 2.9990
chunk 376 optimal weight: 2.9990
chunk 226 optimal weight: 5.9990
chunk 163 optimal weight: 8.9990
chunk 295 optimal weight: 20.0000
chunk 115 optimal weight: 1.9990
chunk 340 optimal weight: 9.9990
chunk 355 optimal weight: 0.9990
chunk 375 optimal weight: 4.9990
overall best weight: 2.7990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 618 GLN
** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 31 HIS
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4005
moved from start: 0.5005
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.080 36386 Z= 0.200
Angle : 0.629 9.533 49818 Z= 0.347
Chirality : 0.042 0.181 5669
Planarity : 0.005 0.140 5925
Dihedral : 19.482 178.359 6091
Min Nonbonded Distance : 1.878
Molprobity Statistics.
All-atom Clashscore : 18.34
Ramachandran Plot:
Outliers : 0.22 %
Allowed : 9.88 %
Favored : 89.90 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 0.65 %
Twisted General : 0.15 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.94 (0.12), residues: 4069
helix: -1.07 (0.12), residues: 1488
sheet: -2.52 (0.22), residues: 446
loop : -2.51 (0.12), residues: 2135
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
401 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 401
time to evaluate : 4.172
Fit side-chains
revert: symmetry clash
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revert: symmetry clash
outliers start: 0
outliers final: 0
residues processed: 401
average time/residue: 1.0641
time to fit residues: 655.7130
Evaluate side-chains
332 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 332
time to evaluate : 4.169
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 5.3002
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 419
random chunks:
chunk 247 optimal weight: 6.9990
chunk 397 optimal weight: 20.0000
chunk 242 optimal weight: 6.9990
chunk 188 optimal weight: 0.7980
chunk 276 optimal weight: 20.0000
chunk 417 optimal weight: 10.0000
chunk 384 optimal weight: 10.0000
chunk 332 optimal weight: 8.9990
chunk 34 optimal weight: 5.9990
chunk 256 optimal weight: 9.9990
chunk 203 optimal weight: 7.9990
overall best weight: 5.7588
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 702 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4098
moved from start: 0.5278
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.068 36386 Z= 0.284
Angle : 0.671 9.492 49818 Z= 0.374
Chirality : 0.042 0.367 5669
Planarity : 0.005 0.068 5925
Dihedral : 19.472 179.951 6091
Min Nonbonded Distance : 1.766
Molprobity Statistics.
All-atom Clashscore : 23.83
Ramachandran Plot:
Outliers : 0.17 %
Allowed : 11.65 %
Favored : 88.18 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 0.65 %
Twisted General : 0.15 %
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: -3.09 (0.12), residues: 4069
helix: -1.20 (0.12), residues: 1488
sheet: -2.54 (0.21), residues: 467
loop : -2.61 (0.12), residues: 2114
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8138 Ramachandran restraints generated.
4069 Oldfield, 0 Emsley, 4069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
371 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 371
time to evaluate : 4.171
Fit side-chains
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 0
outliers final: 0
residues processed: 371
average time/residue: 1.0694
time to fit residues: 608.6995
Evaluate side-chains
320 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 320
time to evaluate : 4.139
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 5.1751
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 419
random chunks:
chunk 264 optimal weight: 7.9990
chunk 354 optimal weight: 0.8980
chunk 101 optimal weight: 2.9990
chunk 306 optimal weight: 1.9990
chunk 49 optimal weight: 0.9990
chunk 92 optimal weight: 10.0000
chunk 332 optimal weight: 2.9990
chunk 139 optimal weight: 5.9990
chunk 341 optimal weight: 4.9990
chunk 42 optimal weight: 10.0000
chunk 61 optimal weight: 7.9990
overall best weight: 1.9788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 31 HIS
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.091354 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.069260 restraints weight = 895003.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.071179 restraints weight = 587925.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.072488 restraints weight = 438019.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start: 0.5377
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.065 36386 Z= 0.187
Angle : 0.614 9.515 49818 Z= 0.338
Chirality : 0.041 0.210 5669
Planarity : 0.005 0.068 5925
Dihedral : 19.320 177.976 6091
Min Nonbonded Distance : 1.902
Molprobity Statistics.
All-atom Clashscore : 17.65
Ramachandran Plot:
Outliers : 0.17 %
Allowed : 8.77 %
Favored : 91.05 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 0.65 %
Twisted General : 0.13 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.71 (0.12), residues: 4069
helix: -0.88 (0.13), residues: 1502
sheet: -2.35 (0.23), residues: 447
loop : -2.39 (0.13), residues: 2120
===============================================================================
Job complete
usr+sys time: 12793.08 seconds
wall clock time: 222 minutes 58.47 seconds (13378.47 seconds total)