Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 11:26:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb6_20288/10_2023/6pb6_20288_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb6_20288/10_2023/6pb6_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_20288/10_2023/6pb6_20288.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb6_20288/10_2023/6pb6_20288.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb6_20288/10_2023/6pb6_20288_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb6_20288/10_2023/6pb6_20288_trim_updated.pdb" } resolution = 4.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.012 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 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. 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 22.08, per 1000 atoms: 0.32 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: 49.44 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: 28.83 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: 24.69 Time building geometry restraints manager: 51.91 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 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.740 Extract box with map and model: 14.380 Check model and map are aligned: 0.750 Set scattering table: 0.490 Process input model: 210.620 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 234.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4037 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 : 10.82 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.59 % Favored : 89.11 % Rotamer: Outliers : 0.11 % Allowed : 3.59 % Favored : 96.29 % 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 : 3.971 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 1.1190 time to fit residues: 1031.4102 Evaluate side-chains 423 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 420 time to evaluate : 3.997 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.6160 time to fit residues: 8.6363 ------------------------------------------------------------------------------- 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** C 760 ASN 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 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4074 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 36302 Z= 0.274 Angle : 0.750 8.717 49688 Z= 0.420 Chirality : 0.043 0.265 5655 Planarity : 0.005 0.083 5922 Dihedral : 19.771 175.624 6056 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.68 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 1.30 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.11), residues: 4069 helix: -2.13 (0.11), residues: 1521 sheet: -3.23 (0.20), residues: 427 loop : -2.95 (0.12), residues: 2121 *********************** 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 502 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 4.021 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 1.0813 time to fit residues: 825.6299 Evaluate side-chains 397 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 4.037 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1131 ------------------------------------------------------------------------------- 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: 10.0000 chunk 118 optimal weight: 7.9990 chunk 316 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 381 optimal weight: 5.9990 chunk 411 optimal weight: 9.9990 chunk 339 optimal weight: 30.0000 chunk 378 optimal weight: 20.0000 chunk 129 optimal weight: 7.9990 chunk 305 optimal weight: 9.9990 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 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN C 622 ASN C 659 GLN C 952 GLN C1157 GLN ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN G 149 ASN ** G 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 GLN H 133 ASN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4267 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 36302 Z= 0.373 Angle : 0.788 8.999 49688 Z= 0.442 Chirality : 0.044 0.290 5655 Planarity : 0.006 0.083 5922 Dihedral : 19.797 179.896 6056 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 24.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.29 % Favored : 87.64 % Rotamer: Outliers : 0.26 % Allowed : 2.62 % Favored : 97.12 % 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: -3.82 (0.11), residues: 4069 helix: -1.88 (0.11), residues: 1517 sheet: -3.03 (0.20), residues: 433 loop : -2.98 (0.11), residues: 2119 *********************** 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 475 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 466 time to evaluate : 4.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 472 average time/residue: 1.0418 time to fit residues: 753.8256 Evaluate side-chains 383 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 380 time to evaluate : 3.984 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5963 time to fit residues: 8.4894 ------------------------------------------------------------------------------- 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: 9.9990 chunk 286 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 255 optimal weight: 10.0000 chunk 382 optimal weight: 5.9990 chunk 405 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 362 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 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 C 658 GLN ** C 659 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 805 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 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4200 moved from start: 0.3631 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= 0.243 Angle : 0.676 8.984 49688 Z= 0.378 Chirality : 0.042 0.284 5655 Planarity : 0.005 0.080 5922 Dihedral : 19.672 179.760 6056 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.73 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: -3.50 (0.11), residues: 4069 helix: -1.58 (0.12), residues: 1538 sheet: -2.97 (0.20), residues: 435 loop : -2.79 (0.12), residues: 2096 *********************** 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 468 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 468 time to evaluate : 4.056 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 outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 1.0404 time to fit residues: 744.5662 Evaluate side-chains 384 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.044 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1478 ------------------------------------------------------------------------------- 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: 0.1980 chunk 229 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 301 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 345 optimal weight: 9.9990 chunk 279 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 363 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 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 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4266 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 36302 Z= 0.276 Angle : 0.678 8.924 49688 Z= 0.380 Chirality : 0.042 0.265 5655 Planarity : 0.005 0.088 5922 Dihedral : 19.637 179.991 6056 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.38 % Favored : 88.55 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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: -3.33 (0.11), residues: 4069 helix: -1.38 (0.12), residues: 1536 sheet: -2.85 (0.21), residues: 432 loop : -2.74 (0.12), residues: 2101 *********************** 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 450 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 450 time to evaluate : 4.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 450 average time/residue: 1.0090 time to fit residues: 705.2410 Evaluate side-chains 378 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 4.068 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0840 ------------------------------------------------------------------------------- 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: 7.9990 chunk 364 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 237 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 chunk 405 optimal weight: 20.0000 chunk 336 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 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 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 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 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: 0.4292 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 36302 Z= 0.273 Angle : 0.675 8.870 49688 Z= 0.379 Chirality : 0.042 0.256 5655 Planarity : 0.005 0.078 5922 Dihedral : 19.630 179.415 6056 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.74 % Favored : 89.19 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: -3.29 (0.11), residues: 4069 helix: -1.34 (0.12), residues: 1542 sheet: -2.81 (0.22), residues: 421 loop : -2.76 (0.12), residues: 2106 *********************** 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 442 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 4.102 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: 442 average time/residue: 0.9919 time to fit residues: 676.2358 Evaluate side-chains 371 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 4.059 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1118 ------------------------------------------------------------------------------- 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: 9.9990 chunk 45 optimal weight: 9.9990 chunk 230 optimal weight: 8.9990 chunk 296 optimal weight: 6.9990 chunk 229 optimal weight: 10.0000 chunk 341 optimal weight: 4.9990 chunk 226 optimal weight: 9.9990 chunk 403 optimal weight: 10.0000 chunk 252 optimal weight: 7.9990 chunk 246 optimal weight: 30.0000 chunk 186 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 GLN ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 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** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN D 651 HIS ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS F 346 GLN ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4449 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 36302 Z= 0.381 Angle : 0.776 8.797 49688 Z= 0.436 Chirality : 0.045 0.252 5655 Planarity : 0.006 0.079 5922 Dihedral : 19.854 177.956 6056 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 30.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.49 % Favored : 86.41 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.08 % 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: -3.63 (0.11), residues: 4069 helix: -1.63 (0.12), residues: 1521 sheet: -2.98 (0.21), residues: 420 loop : -2.92 (0.12), residues: 2128 *********************** 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 416 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 4.066 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 outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 1.0082 time to fit residues: 646.7908 Evaluate side-chains 349 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 4.111 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0751 ------------------------------------------------------------------------------- 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: 6.9990 chunk 241 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 256 optimal weight: 8.9990 chunk 275 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** 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 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 GLN H 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4397 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 36302 Z= 0.290 Angle : 0.694 8.453 49688 Z= 0.389 Chirality : 0.043 0.234 5655 Planarity : 0.005 0.083 5922 Dihedral : 19.859 177.717 6056 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 24.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.50 % Favored : 88.42 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.08 % 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: -3.47 (0.11), residues: 4069 helix: -1.46 (0.12), residues: 1528 sheet: -3.02 (0.21), residues: 427 loop : -2.85 (0.12), residues: 2114 *********************** 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 420 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 4.033 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: 420 average time/residue: 1.0140 time to fit residues: 654.0611 Evaluate side-chains 346 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 4.064 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0991 ------------------------------------------------------------------------------- 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: 7.9990 chunk 386 optimal weight: 20.0000 chunk 352 optimal weight: 10.0000 chunk 376 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 295 optimal weight: 20.0000 chunk 115 optimal weight: 0.6980 chunk 340 optimal weight: 3.9990 chunk 355 optimal weight: 0.9990 chunk 375 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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** D 266 ASN ** 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 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4360 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 36302 Z= 0.239 Angle : 0.654 8.374 49688 Z= 0.365 Chirality : 0.042 0.208 5655 Planarity : 0.005 0.079 5922 Dihedral : 19.804 178.012 6056 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.18 % Favored : 88.74 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -3.19 (0.12), residues: 4069 helix: -1.16 (0.12), residues: 1540 sheet: -2.77 (0.22), residues: 436 loop : -2.77 (0.12), residues: 2093 *********************** 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 427 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 4.419 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 outliers start: 0 outliers final: 0 residues processed: 427 average time/residue: 1.0110 time to fit residues: 666.8504 Evaluate side-chains 356 residues out of total 3505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 4.040 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1884 ------------------------------------------------------------------------------- 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: 7.9990 chunk 397 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 188 optimal weight: 0.7980 chunk 276 optimal weight: 10.0000 chunk 417 optimal weight: 10.0000 chunk 384 optimal weight: 9.9990 chunk 332 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 256 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: