Starting phenix.real_space_refine (version: dev)
on Wed Dec 14 07:02:02 2022 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb6_20288/12_2022/6pb6_20288_trim_updated.pdb
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb6_20288/12_2022/6pb6_20288.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=4.29
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb6_20288/12_2022/6pb6_20288.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb6_20288/12_2022/6pb6_20288.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb6_20288/12_2022/6pb6_20288_trim_updated.pdb"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb6_20288/12_2022/6pb6_20288_trim_updated.pdb"
}
resolution = 4.29
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= -0.012 sd= 0.337
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Convert atoms to be neutral
Process input model
Symmetric amino acids flipped
Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 225": "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 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 810": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D ARG 1355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "F TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Time to flip residues: 0.09s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib"
Total number of atoms: 69824
Number of models: 1
Model: ""
Number of chains: 13
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: 21152
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1340, 21152
Classifications: {'peptide': 1340}
Modifications used: {'COO': 1}
Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283}
Chain: "D"
Number of atoms: 21010
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1337, 21010
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: 7917
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 483, 7917
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: 2482
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 78, 2482
Classifications: {'DNA': 78}
Modifications used: {'3*END': 1}
Link IDs: {'rna3p': 77}
Chain: "2"
Number of atoms: 2488
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 78, 2488
Classifications: {'DNA': 78}
Modifications used: {'3*END': 1}
Link IDs: {'rna3p': 77}
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 29207 SG CYS D 70 120.907 98.806 71.291 1.00 20.00 S
ATOM 29237 SG CYS D 72 121.878 96.074 68.827 1.00 20.00 S
ATOM 29467 SG CYS D 85 119.584 98.477 67.916 1.00 20.00 S
ATOM 29514 SG CYS D 88 117.509 96.073 69.161 1.00 20.00 S
ATOM 41047 SG CYS D 814 67.028 112.786 116.233 1.00 20.00 S
ATOM 42184 SG CYS D 888 67.934 110.057 114.453 1.00 20.00 S
ATOM 42275 SG CYS D 895 69.484 111.838 118.392 1.00 20.00 S
ATOM 42312 SG CYS D 898 66.513 109.970 118.353 1.00 20.00 S
Time building chain proxies: 24.01, per 1000 atoms: 0.34
Number of scatterers: 69824
At special positions: 0
Unit cell: (213.3, 151.2, 204.3, 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 158 15.00
Mg 1 11.99
O 7115 8.00
N 6278 7.00
C 21735 6.00
H 34388 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=0, symmetry=0
Time building additional restraints: 51.11
Conformation dependent library (CDL) restraints added in 4.0 seconds
Dynamic metal coordination
Zn2+ tetrahedral coordination
pdb=" ZN D1501 "
pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 "
pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 "
pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 "
pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 "
pdb=" ZN D1502 "
pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 "
pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 "
pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 "
pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 "
Number of angles added : 12
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:
141 helices and 37 sheets defined
36.6% alpha, 8.5% beta
49 base pairs and 122 stacking pairs defined.
Time for finding SS restraints: 26.21
Creating SS restraints...
Processing helix chain 'A' and resid 35 through 49
removed outlier: 4.785A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A)
removed outlier: 4.348A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A)
removed outlier: 3.677A 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: 4.424A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A)
removed outlier: 3.868A 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 228
Processing helix chain 'C' and resid 5 through 9
Processing helix chain 'C' and resid 29 through 39
Processing helix chain 'C' and resid 49 through 56
Processing helix chain 'C' and resid 82 through 88
Processing helix chain 'C' and resid 206 through 213
Processing helix chain 'C' and resid 217 through 224
Processing helix chain 'C' and resid 243 through 245
No H-bonds generated for 'chain 'C' and resid 243 through 245'
Processing helix chain 'C' and resid 271 through 279
Processing helix chain 'C' and resid 289 through 291
No H-bonds generated for 'chain 'C' and resid 289 through 291'
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: 3.558A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A)
Processing helix chain 'C' and resid 400 through 409
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: 4.513A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A)
Processing helix chain 'C' and resid 496 through 508
Processing helix chain 'C' and resid 520 through 527
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 711
Processing helix chain 'C' and resid 821 through 825
Processing helix chain 'C' and resid 859 through 864
removed outlier: 4.501A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A)
Processing helix chain 'C' and resid 897 through 906
Processing helix chain 'C' and resid 943 through 979
removed outlier: 4.157A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A)
removed outlier: 4.061A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (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 1008 through 1037
removed outlier: 3.595A pdb=" N LYS C1022 " --> pdb=" O TYR C1018 " (cutoff:3.500A)
Processing helix chain 'C' and resid 1082 through 1084
No H-bonds generated for 'chain 'C' and resid 1082 through 1084'
Processing helix chain 'C' and resid 1102 through 1106
Processing helix chain 'C' and resid 1109 through 1134
removed outlier: 3.914A pdb=" N GLU C1114 " --> pdb=" O GLN C1111 " (cutoff:3.500A)
removed outlier: 4.225A pdb=" N ALA C1121 " --> pdb=" O GLY C1118 " (cutoff:3.500A)
removed outlier: 4.004A pdb=" N LYS C1122 " --> pdb=" O MET C1119 " (cutoff:3.500A)
removed outlier: 4.105A pdb=" N GLN C1134 " --> pdb=" O MET C1131 " (cutoff:3.500A)
Processing helix chain 'C' and resid 1138 through 1149
Processing helix chain 'C' and resid 1166 through 1176
Processing helix chain 'C' and resid 1192 through 1202
removed outlier: 4.468A pdb=" N LEU C1198 " --> pdb=" O GLU C1194 " (cutoff:3.500A)
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 1273 through 1281
removed outlier: 3.922A 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 32
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 164 through 172
Processing helix chain 'D' and resid 182 through 191
Processing helix chain 'D' and resid 195 through 207
removed outlier: 3.782A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A)
removed outlier: 3.594A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (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 266 through 283
Processing helix chain 'D' and resid 289 through 307
Processing helix chain 'D' and resid 309 through 311
No H-bonds generated for 'chain 'D' and resid 309 through 311'
Processing helix chain 'D' and resid 328 through 331
Processing helix chain 'D' and resid 337 through 341
Processing helix chain 'D' and resid 370 through 376
Processing helix chain 'D' and resid 378 through 388
Processing helix chain 'D' and resid 394 through 402
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
removed outlier: 3.663A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A)
Processing helix chain 'D' and resid 474 through 483
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 505 through 513
Processing helix chain 'D' and resid 530 through 539
Processing helix chain 'D' and resid 574 through 582
removed outlier: 4.041A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A)
removed outlier: 4.556A 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 612
Processing helix chain 'D' and resid 615 through 634
Processing helix chain 'D' and resid 651 through 670
Processing helix chain 'D' and resid 675 through 699
Processing helix chain 'D' and resid 721 through 727
Processing helix chain 'D' and resid 734 through 740
Processing helix chain 'D' and resid 769 through 788
removed outlier: 4.438A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A)
removed outlier: 4.334A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A)
Processing helix chain 'D' and resid 790 through 804
Processing helix chain 'D' and resid 835 through 838
No H-bonds generated for 'chain 'D' and resid 835 through 838'
Processing helix chain 'D' and resid 866 through 874
Processing helix chain 'D' and resid 916 through 923
Processing helix chain 'D' and resid 926 through 929
Processing helix chain 'D' and resid 1139 through 1145
Processing helix chain 'D' and resid 1217 through 1223
Processing helix chain 'D' and resid 1227 through 1244
removed outlier: 4.043A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A)
Processing helix chain 'D' and resid 1251 through 1260
removed outlier: 4.002A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A)
removed outlier: 3.679A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A)
removed outlier: 3.851A pdb=" N ARG D1258 " --> pdb=" O GLU D1254 " (cutoff:3.500A)
removed outlier: 3.579A pdb=" N GLN D1259 " --> pdb=" O VAL D1255 " (cutoff:3.500A)
Processing helix chain 'D' and resid 1280 through 1286
Processing helix chain 'D' and resid 1309 through 1314
removed outlier: 3.859A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A)
Processing helix chain 'D' and resid 1328 through 1338
removed outlier: 4.249A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A)
Processing helix chain 'D' and resid 1347 through 1352
Processing helix chain 'D' and resid 1363 through 1374
Processing helix chain 'E' and resid 8 through 12
Processing helix chain 'E' and resid 16 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 136
removed outlier: 3.612A pdb=" N ALA F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A)
Processing helix chain 'F' and resid 139 through 141
No H-bonds generated for 'chain 'F' and resid 139 through 141'
Processing helix chain 'F' and resid 144 through 152
removed outlier: 4.030A pdb=" N VAL F 151 " --> pdb=" O GLN F 147 " (cutoff:3.500A)
Processing helix chain 'F' and resid 160 through 164
Processing helix chain 'F' and resid 214 through 220
removed outlier: 3.707A pdb=" N ARG F 218 " --> pdb=" O PRO F 214 " (cutoff:3.500A)
Processing helix chain 'F' and resid 224 through 236
removed outlier: 3.757A pdb=" N TYR F 228 " --> pdb=" O LEU F 224 " (cutoff:3.500A)
removed outlier: 3.551A pdb=" N VAL F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A)
removed outlier: 4.140A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A)
removed outlier: 4.156A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A)
Processing helix chain 'F' and resid 243 through 257
Processing helix chain 'F' and resid 265 through 295
removed outlier: 4.106A pdb=" N MET F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A)
removed outlier: 3.669A pdb=" N ASP F 278 " --> pdb=" O ARG F 274 " (cutoff:3.500A)
removed outlier: 4.235A pdb=" N GLN F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A)
Processing helix chain 'F' and resid 300 through 308
Processing helix chain 'F' and resid 316 through 320
Processing helix chain 'F' and resid 325 through 351
removed outlier: 4.020A pdb=" N ASP F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A)
removed outlier: 5.131A pdb=" N VAL F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A)
removed outlier: 3.833A pdb=" N SER F 334 " --> pdb=" O LEU F 330 " (cutoff:3.500A)
removed outlier: 5.202A pdb=" N GLU F 335 " --> pdb=" O HIS F 331 " (cutoff:3.500A)
removed outlier: 5.854A pdb=" N GLU F 336 " --> pdb=" O ASP F 332 " (cutoff:3.500A)
removed outlier: 3.740A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A)
removed outlier: 3.664A pdb=" N ILE F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A)
removed outlier: 4.116A pdb=" N GLU F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A)
removed outlier: 3.758A pdb=" N GLU F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A)
Processing helix chain 'F' and resid 355 through 382
removed outlier: 4.392A pdb=" N ARG F 363 " --> pdb=" O LYS F 359 " (cutoff:3.500A)
removed outlier: 4.303A pdb=" N ALA F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A)
removed outlier: 4.760A pdb=" N LYS F 377 " --> pdb=" O ARG F 373 " (cutoff:3.500A)
removed outlier: 3.937A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A)
removed outlier: 3.912A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A)
Processing helix chain 'F' and resid 384 through 393
removed outlier: 3.857A pdb=" N LYS F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A)
Processing helix chain 'F' and resid 401 through 416
Processing helix chain 'F' and resid 428 through 445
removed outlier: 3.626A pdb=" N ARG F 436 " --> pdb=" O THR F 432 " (cutoff:3.500A)
removed outlier: 4.122A pdb=" N ALA F 444 " --> pdb=" O THR F 440 " (cutoff:3.500A)
Processing helix chain 'F' and resid 454 through 474
removed outlier: 3.719A pdb=" N ARG F 468 " --> pdb=" O ASN F 464 " (cutoff:3.500A)
Processing helix chain 'F' and resid 480 through 486
Processing helix chain 'F' and resid 491 through 499
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: 4.150A pdb=" N GLY F 550 " --> pdb=" O ASP F 546 " (cutoff:3.500A)
Processing helix chain 'F' and resid 553 through 561
removed outlier: 3.637A pdb=" N LYS F 557 " --> pdb=" O ALA F 553 " (cutoff:3.500A)
removed outlier: 4.267A pdb=" N VAL F 558 " --> pdb=" O ARG F 554 " (cutoff:3.500A)
Processing helix chain 'F' and resid 575 through 579
Processing helix chain 'F' and resid 586 through 598
Processing helix chain 'F' and resid 604 through 608
Processing helix chain 'G' and resid 10 through 17
removed outlier: 3.563A pdb=" N PHE G 14 " --> pdb=" O THR G 10 " (cutoff:3.500A)
Processing helix chain 'G' and resid 99 through 108
Processing helix chain 'G' and resid 113 through 136
removed outlier: 3.957A pdb=" N ALA G 135 " --> pdb=" O VAL G 131 " (cutoff:3.500A)
Processing helix chain 'G' and resid 139 through 151
Processing helix chain 'G' and resid 171 through 176
Processing helix chain 'G' and resid 180 through 193
Processing helix chain 'H' and resid 10 through 16
Processing helix chain 'H' and resid 72 through 74
No H-bonds generated for 'chain 'H' and resid 72 through 74'
Processing helix chain 'H' and resid 99 through 108
Processing helix chain 'H' and resid 111 through 136
removed outlier: 4.291A pdb=" N SER H 117 " --> pdb=" O MET H 114 " (cutoff:3.500A)
removed outlier: 4.160A pdb=" N SER H 128 " --> pdb=" O GLN H 125 " (cutoff:3.500A)
Processing helix chain 'H' and resid 139 through 152
removed outlier: 3.854A pdb=" N ASN H 149 " --> pdb=" O GLN H 145 " (cutoff:3.500A)
removed outlier: 4.166A pdb=" N LYS H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A)
Processing helix chain 'H' and resid 170 through 175
removed outlier: 3.873A pdb=" N GLN H 174 " --> pdb=" O GLN H 170 " (cutoff:3.500A)
Processing helix chain 'H' and resid 180 through 192
Processing sheet with id= A, first strand: chain 'A' and resid 24 through 26
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: 5.447A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A)
removed outlier: 4.822A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A)
removed outlier: 7.112A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A)
removed outlier: 5.523A 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
removed outlier: 3.642A pdb=" N GLY A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A)
Processing sheet with id= E, first strand: chain 'B' and resid 182 through 186
removed outlier: 3.712A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A)
removed outlier: 6.450A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A)
removed outlier: 4.642A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A)
Processing sheet with id= F, first strand: chain 'B' and resid 97 through 104
removed outlier: 6.606A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A)
removed outlier: 5.334A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A)
removed outlier: 6.488A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A)
removed outlier: 4.808A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A)
Processing sheet with id= G, first strand: chain 'C' and resid 12 through 14
No H-bonds generated for sheet with id= G
Processing sheet with id= H, first strand: chain 'C' and resid 73 through 75
Processing sheet with id= I, first strand: chain 'C' and resid 148 through 151
Processing sheet with id= J, first strand: chain 'C' and resid 154 through 161
Processing sheet with id= K, first strand: chain 'C' and resid 185 through 188
Processing sheet with id= L, first strand: chain 'C' and resid 333 through 336
removed outlier: 5.394A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A)
removed outlier: 4.149A pdb=" N LYS C 236 " --> pdb=" O ARG C 233 " (cutoff:3.500A)
removed outlier: 3.868A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A)
Processing sheet with id= M, first strand: chain 'C' and resid 634 through 638
Processing sheet with id= N, first strand: chain 'C' and resid 750 through 752
removed outlier: 5.562A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A)
removed outlier: 5.315A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A)
Processing sheet with id= O, first strand: chain 'C' and resid 798 through 803
removed outlier: 3.731A pdb=" N GLY C1228 " --> pdb=" O VAL C 802 " (cutoff:3.500A)
Processing sheet with id= P, first strand: chain 'C' and resid 830 through 832
Processing sheet with id= Q, first strand: chain 'C' and resid 887 through 889
Processing sheet with id= R, first strand: chain 'C' and resid 835 through 841
removed outlier: 3.634A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A)
removed outlier: 5.971A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A)
removed outlier: 5.377A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A)
Processing sheet with id= S, first strand: chain 'D' and resid 104 through 106
Processing sheet with id= T, first strand: chain 'D' and resid 252 through 255
Processing sheet with id= U, first strand: chain 'D' and resid 351 through 354
removed outlier: 3.795A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A)
Processing sheet with id= V, first strand: chain 'D' and resid 421 through 424
Processing sheet with id= W, first strand: chain 'D' and resid 547 through 554
Processing sheet with id= X, first strand: chain 'D' and resid 948 through 950
Processing sheet with id= Y, first strand: chain 'D' and resid 965 through 967
Processing sheet with id= Z, first strand: chain 'D' and resid 1113 through 1115
removed outlier: 3.593A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A)
removed outlier: 3.787A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A)
Processing sheet with id= AA, first strand: chain 'D' and resid 1105 through 1107
Processing sheet with id= AB, first strand: chain 'D' and resid 1162 through 1165
Processing sheet with id= AC, first strand: chain 'D' and resid 1264 through 1266
Processing sheet with id= AD, first strand: chain 'D' and resid 145 through 148
removed outlier: 6.722A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A)
Processing sheet with id= AE, first strand: chain 'D' and resid 981 through 985
Processing sheet with id= AF, first strand: chain 'G' and resid 21 through 23
removed outlier: 3.506A pdb=" N HIS G 21 " --> pdb=" O VAL G 94 " (cutoff:3.500A)
removed outlier: 6.026A pdb=" N ALA G 95 " --> pdb=" O ILE G 42 " (cutoff:3.500A)
removed outlier: 5.383A pdb=" N ILE G 42 " --> pdb=" O ALA G 95 " (cutoff:3.500A)
removed outlier: 6.710A pdb=" N ILE G 97 " --> pdb=" O TYR G 40 " (cutoff:3.500A)
removed outlier: 5.170A pdb=" N TYR G 40 " --> pdb=" O ILE G 97 " (cutoff:3.500A)
Processing sheet with id= AG, first strand: chain 'G' and resid 85 through 88
removed outlier: 3.622A pdb=" N ILE G 51 " --> pdb=" O MET G 59 " (cutoff:3.500A)
removed outlier: 4.871A pdb=" N LYS G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A)
Processing sheet with id= AH, first strand: chain 'G' and resid 163 through 165
Processing sheet with id= AI, first strand: chain 'H' and resid 21 through 23
Processing sheet with id= AJ, first strand: chain 'H' and resid 85 through 88
removed outlier: 6.308A pdb=" N ILE H 51 " --> pdb=" O ILE H 60 " (cutoff:3.500A)
removed outlier: 4.725A pdb=" N ILE H 60 " --> pdb=" O ILE H 51 " (cutoff:3.500A)
Processing sheet with id= AK, first strand: chain 'H' and resid 163 through 165
1089 hydrogen bonds defined for protein.
3009 hydrogen bond angles defined for protein.
Restraints generated for nucleic acids:
117 hydrogen bonds
234 hydrogen bond angles
0 basepair planarities
49 basepair parallelities
122 stacking parallelities
Total time for adding SS restraints: 26.33
Time building geometry restraints manager: 53.06 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
0.83 - 1.02: 34358
1.02 - 1.22: 104
1.22 - 1.42: 14706
1.42 - 1.62: 21258
1.62 - 1.82: 264
Bond restraints: 70690
Sorted by residual:
bond pdb=" C3' DG 2 42 "
pdb=" O3' DG 2 42 "
ideal model delta sigma weight residual
1.422 1.554 -0.132 3.00e-02 1.11e+03 1.93e+01
bond pdb=" C GLY F 239 "
pdb=" O GLY F 239 "
ideal model delta sigma weight residual
1.236 1.214 0.022 5.30e-03 3.56e+04 1.68e+01
bond pdb=" CA VAL C1103 "
pdb=" CB VAL C1103 "
ideal model delta sigma weight residual
1.539 1.521 0.018 5.40e-03 3.43e+04 1.16e+01
bond pdb=" CA LEU D1261 "
pdb=" CB LEU D1261 "
ideal model delta sigma weight residual
1.531 1.428 0.103 3.12e-02 1.03e+03 1.08e+01
bond pdb=" CA ARG D 53 "
pdb=" CB ARG D 53 "
ideal model delta sigma weight residual
1.534 1.467 0.068 2.33e-02 1.84e+03 8.44e+00
... (remaining 70685 not shown)
Histogram of bond angle deviations from ideal:
95.68 - 103.86: 898
103.86 - 112.04: 81139
112.04 - 120.22: 25178
120.22 - 128.41: 20609
128.41 - 136.59: 415
Bond angle restraints: 128239
Sorted by residual:
angle pdb=" O4' DG 2 42 "
pdb=" C1' DG 2 42 "
pdb=" N9 DG 2 42 "
ideal model delta sigma weight residual
108.40 117.86 -9.46 1.50e+00 4.44e-01 3.98e+01
angle pdb=" N ILE G 112 "
pdb=" CA ILE G 112 "
pdb=" C ILE G 112 "
ideal model delta sigma weight residual
112.96 106.98 5.98 1.00e+00 1.00e+00 3.57e+01
angle pdb=" C4' DG 2 42 "
pdb=" O4' DG 2 42 "
pdb=" C1' DG 2 42 "
ideal model delta sigma weight residual
109.70 101.26 8.44 1.50e+00 4.44e-01 3.17e+01
angle pdb=" N PHE C 812 "
pdb=" CA PHE C 812 "
pdb=" C PHE C 812 "
ideal model delta sigma weight residual
111.02 117.43 -6.41 1.22e+00 6.72e-01 2.76e+01
angle pdb=" CA TYR F 143 "
pdb=" CB TYR F 143 "
pdb=" CG TYR F 143 "
ideal model delta sigma weight residual
113.90 123.35 -9.45 1.80e+00 3.09e-01 2.76e+01
... (remaining 128234 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 35.98: 26614
35.98 - 71.95: 917
71.95 - 107.93: 22
107.93 - 143.91: 5
143.91 - 179.88: 9
Dihedral angle restraints: 27567
sinusoidal: 14474
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 -119.66 -60.34 0 5.00e+00 4.00e-02 1.46e+02
dihedral pdb=" CA ILE H 167 "
pdb=" C ILE H 167 "
pdb=" N THR H 168 "
pdb=" CA THR H 168 "
ideal model delta harmonic sigma weight residual
-180.00 -126.58 -53.42 0 5.00e+00 4.00e-02 1.14e+02
dihedral pdb=" CA VAL A 153 "
pdb=" C VAL A 153 "
pdb=" N PRO A 154 "
pdb=" CA PRO A 154 "
ideal model delta harmonic sigma weight residual
-180.00 -126.81 -53.19 0 5.00e+00 4.00e-02 1.13e+02
... (remaining 27564 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.075: 4705
0.075 - 0.150: 892
0.150 - 0.224: 53
0.224 - 0.299: 4
0.299 - 0.374: 1
Chirality restraints: 5655
Sorted by residual:
chirality pdb=" C1' DG 2 42 "
pdb=" O4' DG 2 42 "
pdb=" C2' DG 2 42 "
pdb=" N9 DG 2 42 "
both_signs ideal model delta sigma weight residual
False 2.42 2.05 0.37 2.00e-01 2.50e+01 3.49e+00
chirality pdb=" P DG 2 42 "
pdb=" OP1 DG 2 42 "
pdb=" OP2 DG 2 42 "
pdb=" O5' DG 2 42 "
both_signs ideal model delta sigma weight residual
True 2.35 -2.62 -0.27 2.00e-01 2.50e+01 1.82e+00
chirality pdb=" CB VAL D 574 "
pdb=" CA VAL D 574 "
pdb=" CG1 VAL D 574 "
pdb=" CG2 VAL D 574 "
both_signs ideal model delta sigma weight residual
False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00
... (remaining 5652 not shown)
Planarity restraints: 9955
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C1' DG 2 42 " 0.065 2.00e-02 2.50e+03 2.60e-02 2.37e+01
pdb=" N9 DG 2 42 " -0.065 2.00e-02 2.50e+03
pdb=" C8 DG 2 42 " -0.002 2.00e-02 2.50e+03
pdb=" N7 DG 2 42 " -0.001 2.00e-02 2.50e+03
pdb=" C5 DG 2 42 " 0.018 2.00e-02 2.50e+03
pdb=" C6 DG 2 42 " 0.010 2.00e-02 2.50e+03
pdb=" O6 DG 2 42 " 0.003 2.00e-02 2.50e+03
pdb=" N1 DG 2 42 " 0.007 2.00e-02 2.50e+03
pdb=" C2 DG 2 42 " -0.011 2.00e-02 2.50e+03
pdb=" N2 DG 2 42 " -0.005 2.00e-02 2.50e+03
pdb=" N3 DG 2 42 " -0.017 2.00e-02 2.50e+03
pdb=" C4 DG 2 42 " -0.005 2.00e-02 2.50e+03
pdb=" H8 DG 2 42 " -0.007 2.00e-02 2.50e+03
pdb=" H1 DG 2 42 " 0.009 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C LEU D 120 " 0.063 5.00e-02 4.00e+02 9.59e-02 1.47e+01
pdb=" N PRO D 121 " -0.166 5.00e-02 4.00e+02
pdb=" CA PRO D 121 " 0.051 5.00e-02 4.00e+02
pdb=" CD PRO D 121 " 0.052 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" C ILE D1357 " -0.059 5.00e-02 4.00e+02 8.91e-02 1.27e+01
pdb=" N PRO D1358 " 0.154 5.00e-02 4.00e+02
pdb=" CA PRO D1358 " -0.046 5.00e-02 4.00e+02
pdb=" CD PRO D1358 " -0.048 5.00e-02 4.00e+02
... (remaining 9952 not shown)
Histogram of nonbonded interaction distances:
1.26 - 1.93: 521
1.93 - 2.60: 84619
2.60 - 3.26: 214528
3.26 - 3.93: 265287
3.93 - 4.60: 412008
Nonbonded interactions: 976963
Sorted by model distance:
nonbonded pdb=" HA LYS G 52 "
pdb=" HG3 GLU G 58 "
model vdw
1.261 2.440
nonbonded pdb="HG12 VAL G 94 "
pdb=" HG3 GLU G 96 "
model vdw
1.348 2.440
nonbonded pdb=" HD1 TYR G 40 "
pdb=" HG2 GLU G 96 "
model vdw
1.550 2.270
nonbonded pdb=" HE ARG F 554 "
pdb=" OE2 GLU F 555 "
model vdw
1.571 1.850
nonbonded pdb=" O LYS D1286 "
pdb=" H ARG D1290 "
model vdw
1.582 1.850
... (remaining 976958 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 158 5.49 5
Mg 1 5.21 5
S 147 5.16 5
C 21735 2.51 5
N 6278 2.21 5
O 7115 1.98 5
H 34388 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: 2.390
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.010
Construct map_model_manager: 0.750
Extract box with map and model: 15.460
Check model and map are aligned: 0.770
Convert atoms to be neutral: 0.470
Process input model: 211.240
Find NCS groups from input model: 1.400
Set up NCS constraints: 0.210
Set refine NCS operators: 0.000
Set scattering table: 0.030
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:2.440
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 235.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3879
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 0.132 36302 Z= 0.622
Angle : 1.126 11.281 49688 Z= 0.638
Chirality : 0.055 0.374 5655
Planarity : 0.007 0.096 5922
Dihedral : 16.039 179.883 14167
Min Nonbonded Distance : 1.968
Molprobity Statistics.
All-atom Clashscore : 10.87
Ramachandran Plot:
Outliers : 0.29 %
Allowed : 10.59 %
Favored : 89.11 %
Rotamer Outliers : 0.11 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 1.95 %
Twisted General : 0.53 %
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: -4.79 (0.10), residues: 4069
helix: -3.06 (0.09), residues: 1488
sheet: -3.55 (0.20), residues: 380
loop : -3.25 (0.11), residues: 2201
*********************** 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
608 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 4
poor density : 604
time to evaluate : 4.091
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
outliers start: 4
outliers final: 3
residues processed: 607
average time/residue: 1.0319
time to fit residues: 958.8830
Evaluate side-chains
423 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 3
poor density : 420
time to evaluate : 4.019
Switching outliers to nearest non-outliers
outliers start: 3
outliers final: 0
residues processed: 3
average time/residue: 0.5866
time to fit residues: 8.4083
-------------------------------------------------------------------------------
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: 6.9990
chunk 317 optimal weight: 10.0000
chunk 176 optimal weight: 8.9990
chunk 108 optimal weight: 3.9990
chunk 214 optimal weight: 0.9990
chunk 169 optimal weight: 6.9990
chunk 328 optimal weight: 5.9990
chunk 127 optimal weight: 2.9990
chunk 199 optimal weight: 7.9990
chunk 244 optimal weight: 10.0000
chunk 380 optimal weight: 10.0000
overall best weight: 4.1990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
C 510 GLN
C 568 ASN
C 620 ASN
** C 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1017 GLN
C1313 HIS
D 186 GLN
** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 817 HIS
F 169 ASN
F 383 ASN
F 409 ASN
F 464 ASN
** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 145 GLN
Total number of N/Q/H flips: 12
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3876
moved from start: 0.2106
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.075 36302 Z= 0.267
Angle : 0.741 8.644 49688 Z= 0.415
Chirality : 0.043 0.267 5655
Planarity : 0.005 0.084 5922
Dihedral : 19.751 175.215 6056
Min Nonbonded Distance : 1.787
Molprobity Statistics.
All-atom Clashscore : 18.37
Ramachandran Plot:
Outliers : 0.12 %
Allowed : 9.58 %
Favored : 90.29 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 1.30 %
Twisted General : 0.18 %
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: -3.95 (0.11), residues: 4069
helix: -2.09 (0.11), residues: 1523
sheet: -3.13 (0.20), residues: 417
loop : -2.96 (0.12), residues: 2129
*********************** 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
504 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 504
time to evaluate : 4.049
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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 0
outliers final: 0
residues processed: 504
average time/residue: 1.0173
time to fit residues: 783.3011
Evaluate side-chains
394 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 394
time to evaluate : 4.037
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 5.1030
-------------------------------------------------------------------------------
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: 6.9990
chunk 118 optimal weight: 9.9990
chunk 316 optimal weight: 6.9990
chunk 259 optimal weight: 9.9990
chunk 104 optimal weight: 1.9990
chunk 381 optimal weight: 6.9990
chunk 411 optimal weight: 9.9990
chunk 339 optimal weight: 30.0000
chunk 378 optimal weight: 9.9990
chunk 129 optimal weight: 2.9990
chunk 305 optimal weight: 6.9990
overall best weight: 5.1990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 517 GLN
C1257 GLN
** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 80 GLN
** G 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 133 ASN
** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3957
moved from start: 0.2870
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.005 0.111 36302 Z= 0.296
Angle : 0.722 9.250 49688 Z= 0.405
Chirality : 0.043 0.297 5655
Planarity : 0.005 0.082 5922
Dihedral : 19.664 178.998 6056
Min Nonbonded Distance : 1.818
Molprobity Statistics.
All-atom Clashscore : 19.11
Ramachandran Plot:
Outliers : 0.07 %
Allowed : 10.74 %
Favored : 89.19 %
Rotamer Outliers : 0.14 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 1.30 %
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: -3.69 (0.11), residues: 4069
helix: -1.77 (0.11), residues: 1529
sheet: -2.99 (0.20), residues: 433
loop : -2.89 (0.12), residues: 2107
*********************** 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
465 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 5
poor density : 460
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
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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
outliers start: 5
outliers final: 1
residues processed: 463
average time/residue: 1.0111
time to fit residues: 724.4143
Evaluate side-chains
384 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 383
time to evaluate : 4.113
Switching outliers to nearest non-outliers
outliers start: 1
outliers final: 0
residues processed: 1
average time/residue: 0.5951
time to fit residues: 6.3765
-------------------------------------------------------------------------------
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: 8.9990
chunk 197 optimal weight: 8.9990
chunk 42 optimal weight: 9.9990
chunk 181 optimal weight: 10.0000
chunk 255 optimal weight: 9.9990
chunk 382 optimal weight: 4.9990
chunk 405 optimal weight: 20.0000
chunk 199 optimal weight: 6.9990
chunk 362 optimal weight: 5.9990
chunk 109 optimal weight: 8.9990
overall best weight: 6.5990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 622 ASN
C 760 ASN
** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 952 GLN
C1157 GLN
** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 242 HIS
** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 518 HIS
G 149 ASN
** G 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 66 GLN
** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4066
moved from start: 0.3657
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.005 0.116 36302 Z= 0.340
Angle : 0.743 8.972 49688 Z= 0.416
Chirality : 0.043 0.291 5655
Planarity : 0.005 0.081 5922
Dihedral : 19.726 179.701 6056
Min Nonbonded Distance : 1.814
Molprobity Statistics.
All-atom Clashscore : 24.12
Ramachandran Plot:
Outliers : 0.07 %
Allowed : 11.65 %
Favored : 88.28 %
Rotamer Outliers : 0.09 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 1.30 %
Twisted General : 0.10 %
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: -3.68 (0.11), residues: 4069
helix: -1.77 (0.11), residues: 1528
sheet: -3.01 (0.20), residues: 437
loop : -2.87 (0.12), residues: 2104
*********************** 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
461 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 3
poor density : 458
time to evaluate : 4.164
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
outliers start: 3
outliers final: 1
residues processed: 461
average time/residue: 0.9891
time to fit residues: 706.4089
Evaluate side-chains
376 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 375
time to evaluate : 4.078
Switching outliers to nearest non-outliers
outliers start: 1
outliers final: 0
residues processed: 1
average time/residue: 0.5639
time to fit residues: 6.1727
-------------------------------------------------------------------------------
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: 0.4980
chunk 229 optimal weight: 7.9990
chunk 5 optimal weight: 7.9990
chunk 301 optimal weight: 6.9990
chunk 167 optimal weight: 9.9990
chunk 345 optimal weight: 0.9990
chunk 279 optimal weight: 8.9990
chunk 0 optimal weight: 10.0000
chunk 206 optimal weight: 7.9990
chunk 363 optimal weight: 9.9990
chunk 102 optimal weight: 10.0000
overall best weight: 4.8988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 17 HIS
** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4032
moved from start: 0.4152
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.070 36302 Z= 0.262
Angle : 0.679 9.117 49688 Z= 0.380
Chirality : 0.042 0.279 5655
Planarity : 0.005 0.093 5922
Dihedral : 19.656 179.368 6056
Min Nonbonded Distance : 1.846
Molprobity Statistics.
All-atom Clashscore : 19.44
Ramachandran Plot:
Outliers : 0.07 %
Allowed : 10.22 %
Favored : 89.70 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 0.65 %
Twisted General : 0.10 %
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: -3.40 (0.11), residues: 4069
helix: -1.48 (0.12), residues: 1541
sheet: -2.88 (0.21), residues: 436
loop : -2.76 (0.12), residues: 2092
*********************** 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
447 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 447
time to evaluate : 4.179
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
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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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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: 447
average time/residue: 0.9539
time to fit residues: 662.4592
Evaluate side-chains
375 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 375
time to evaluate : 4.027
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 5.0678
-------------------------------------------------------------------------------
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: 0.0980
chunk 364 optimal weight: 6.9990
chunk 80 optimal weight: 3.9990
chunk 237 optimal weight: 7.9990
chunk 99 optimal weight: 9.9990
chunk 405 optimal weight: 20.0000
chunk 336 optimal weight: 10.0000
chunk 187 optimal weight: 9.9990
chunk 33 optimal weight: 3.9990
chunk 134 optimal weight: 0.9990
chunk 212 optimal weight: 5.9990
overall best weight: 3.0188
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 242 HIS
** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 518 HIS
** G 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3986
moved from start: 0.4390
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.067 36302 Z= 0.211
Angle : 0.636 8.894 49688 Z= 0.355
Chirality : 0.041 0.254 5655
Planarity : 0.004 0.077 5922
Dihedral : 19.568 179.888 6056
Min Nonbonded Distance : 1.843
Molprobity Statistics.
All-atom Clashscore : 17.81
Ramachandran Plot:
Outliers : 0.07 %
Allowed : 9.63 %
Favored : 90.29 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 0.65 %
Twisted General : 0.05 %
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: -1.18 (0.12), residues: 1533
sheet: -2.81 (0.21), residues: 427
loop : -2.59 (0.12), residues: 2109
*********************** 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
449 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 449
time to evaluate : 4.163
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
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revert: symmetry clash
revert: symmetry clash
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
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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
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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
outliers start: 0
outliers final: 0
residues processed: 449
average time/residue: 0.9603
time to fit residues: 668.3023
Evaluate side-chains
376 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 376
time to evaluate : 4.183
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 5.2458
-------------------------------------------------------------------------------
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: 10.0000
chunk 45 optimal weight: 9.9990
chunk 230 optimal weight: 7.9990
chunk 296 optimal weight: 9.9990
chunk 229 optimal weight: 8.9990
chunk 341 optimal weight: 9.9990
chunk 226 optimal weight: 10.0000
chunk 403 optimal weight: 5.9990
chunk 252 optimal weight: 0.9990
chunk 246 optimal weight: 30.0000
chunk 186 optimal weight: 3.9990
overall best weight: 5.5990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
C 219 GLN
** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 242 HIS
** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4104
moved from start: 0.4873
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.005 0.107 36302 Z= 0.305
Angle : 0.699 8.707 49688 Z= 0.393
Chirality : 0.043 0.241 5655
Planarity : 0.005 0.077 5922
Dihedral : 19.628 179.366 6056
Min Nonbonded Distance : 1.800
Molprobity Statistics.
All-atom Clashscore : 22.91
Ramachandran Plot:
Outliers : 0.07 %
Allowed : 11.87 %
Favored : 88.06 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 0.65 %
Twisted General : 0.05 %
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: -3.27 (0.12), residues: 4069
helix: -1.35 (0.12), residues: 1536
sheet: -2.84 (0.21), residues: 421
loop : -2.70 (0.12), residues: 2112
*********************** 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
435 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 435
time to evaluate : 4.098
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
outliers start: 0
outliers final: 0
residues processed: 435
average time/residue: 0.9584
time to fit residues: 648.8560
Evaluate side-chains
364 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 364
time to evaluate : 4.736
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 5.9158
-------------------------------------------------------------------------------
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: 9.9990
chunk 161 optimal weight: 3.9990
chunk 241 optimal weight: 9.9990
chunk 121 optimal weight: 5.9990
chunk 79 optimal weight: 0.4980
chunk 78 optimal weight: 0.8980
chunk 256 optimal weight: 8.9990
chunk 275 optimal weight: 10.0000
chunk 199 optimal weight: 8.9990
chunk 37 optimal weight: 9.9990
chunk 317 optimal weight: 9.9990
overall best weight: 4.0786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1009 ASN
** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1259 GLN
F 242 HIS
** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 119 GLN
** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4050
moved from start: 0.5141
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.064 36302 Z= 0.231
Angle : 0.642 8.299 49688 Z= 0.358
Chirality : 0.041 0.223 5655
Planarity : 0.005 0.075 5922
Dihedral : 19.596 179.008 6056
Min Nonbonded Distance : 1.811
Molprobity Statistics.
All-atom Clashscore : 19.43
Ramachandran Plot:
Outliers : 0.07 %
Allowed : 9.71 %
Favored : 90.22 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 0.65 %
Twisted General : 0.05 %
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: -3.03 (0.12), residues: 4069
helix: -1.09 (0.12), residues: 1542
sheet: -2.76 (0.22), residues: 412
loop : -2.61 (0.12), residues: 2115
*********************** 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
441 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 441
time to evaluate : 4.123
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
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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: 441
average time/residue: 0.9589
time to fit residues: 656.8947
Evaluate side-chains
372 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 372
time to evaluate : 4.141
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 5.2491
-------------------------------------------------------------------------------
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: 6.9990
chunk 386 optimal weight: 20.0000
chunk 352 optimal weight: 1.9990
chunk 376 optimal weight: 1.9990
chunk 226 optimal weight: 10.0000
chunk 163 optimal weight: 4.9990
chunk 295 optimal weight: 10.0000
chunk 115 optimal weight: 7.9990
chunk 340 optimal weight: 9.9990
chunk 355 optimal weight: 4.9990
chunk 375 optimal weight: 8.9990
overall best weight: 4.1990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1017 GLN
** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 242 HIS
** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 17 HIS
** H 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 164 GLN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4075
moved from start: 0.5448
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.074 36302 Z= 0.243
Angle : 0.643 8.024 49688 Z= 0.359
Chirality : 0.042 0.200 5655
Planarity : 0.005 0.076 5922
Dihedral : 19.589 179.142 6056
Min Nonbonded Distance : 1.822
Molprobity Statistics.
All-atom Clashscore : 19.86
Ramachandran Plot:
Outliers : 0.07 %
Allowed : 10.86 %
Favored : 89.06 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 0.65 %
Twisted General : 0.03 %
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: -2.97 (0.12), residues: 4069
helix: -0.99 (0.12), residues: 1549
sheet: -2.77 (0.22), residues: 423
loop : -2.61 (0.12), residues: 2097
*********************** 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
442 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 442
time to evaluate : 4.136
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
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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
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
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
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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
outliers start: 0
outliers final: 0
residues processed: 442
average time/residue: 0.9898
time to fit residues: 679.2899
Evaluate side-chains
363 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 363
time to evaluate : 4.130
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 5.3707
-------------------------------------------------------------------------------
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: 20.0000
chunk 397 optimal weight: 6.9990
chunk 242 optimal weight: 0.8980
chunk 188 optimal weight: 2.9990
chunk 276 optimal weight: 9.9990
chunk 417 optimal weight: 10.0000
chunk 384 optimal weight: 0.0980
chunk 332 optimal weight: 3.9990
chunk 34 optimal weight: 10.0000
chunk 256 optimal weight: 10.0000
chunk 203 optimal weight: 10.0000
overall best weight: 2.9986
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 242 HIS
** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4029
moved from start: 0.5614
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.059 36302 Z= 0.200
Angle : 0.616 8.131 49688 Z= 0.342
Chirality : 0.041 0.184 5655
Planarity : 0.004 0.065 5922
Dihedral : 19.579 179.012 6056
Min Nonbonded Distance : 1.851
Molprobity Statistics.
All-atom Clashscore : 17.94
Ramachandran Plot:
Outliers : 0.07 %
Allowed : 8.92 %
Favored : 91.01 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 0.65 %
Twisted General : 0.05 %
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: -0.77 (0.12), residues: 1547
sheet: -2.51 (0.23), residues: 404
loop : -2.50 (0.12), residues: 2118
********************** 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
447 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 447
time to evaluate : 4.115
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
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revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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
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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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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: 447
average time/residue: 0.9667
time to fit residues: 671.0129
Evaluate side-chains
362 residues out of total 3505 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 362
time to evaluate : 4.035
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 5.0911
-------------------------------------------------------------------------------
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: 0.9990
chunk 354 optimal weight: 0.1980
chunk 101 optimal weight: 0.0010
chunk 306 optimal weight: 7.9990
chunk 49 optimal weight: 1.9990
chunk 92 optimal weight: 8.9990
chunk 332 optimal weight: 0.9990
chunk 139 optimal weight: 9.9990
chunk 341 optimal weight: 7.9990
chunk 42 optimal weight: 10.0000
chunk 61 optimal weight: 5.9990
overall best weight: 0.8392
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
C 219 GLN
** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.101518 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.077769 restraints weight = 783762.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.079582 restraints weight = 525463.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.080931 restraints weight = 402907.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start: 0.5798
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.056 36302 Z= 0.163
Angle : 0.594 8.170 49688 Z= 0.326
Chirality : 0.041 0.194 5655
Planarity : 0.004 0.065 5922
Dihedral : 19.442 179.951 6056
Min Nonbonded Distance : 1.904
Molprobity Statistics.
All-atom Clashscore : 14.22
Ramachandran Plot:
Outliers : 0.07 %
Allowed : 7.94 %
Favored : 91.99 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.60 %
Cis-general : 0.00 %
Twisted Proline : 0.65 %
Twisted General : 0.03 %
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: -2.27 (0.12), residues: 4069
helix: -0.40 (0.13), residues: 1570
sheet: -2.23 (0.23), residues: 434
loop : -2.25 (0.13), residues: 2065
===============================================================================
Job complete
usr+sys time: 13621.19 seconds
wall clock time: 236 minutes 55.48 seconds (14215.48 seconds total)