Starting phenix.real_space_refine on Thu Feb 15 13:45:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm3_30400/02_2024/7cm3_30400_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm3_30400/02_2024/7cm3_30400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm3_30400/02_2024/7cm3_30400.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm3_30400/02_2024/7cm3_30400.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm3_30400/02_2024/7cm3_30400_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm3_30400/02_2024/7cm3_30400_updated.pdb" } resolution = 3.1 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= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 96 5.16 5 C 8194 2.51 5 N 1956 2.21 5 O 2162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 43": "NH1" <-> "NH2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ARG 382": "NH1" <-> "NH2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A ARG 851": "NH1" <-> "NH2" Residue "A ARG 855": "NH1" <-> "NH2" Residue "A ARG 857": "NH1" <-> "NH2" Residue "A ARG 911": "NH1" <-> "NH2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "A ARG 951": "NH1" <-> "NH2" Residue "A ARG 992": "NH1" <-> "NH2" Residue "A PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1004": "NH1" <-> "NH2" Residue "A ARG 1008": "NH1" <-> "NH2" Residue "A GLU 1009": "OE1" <-> "OE2" Residue "A GLU 1016": "OE1" <-> "OE2" Residue "A ARG 1062": "NH1" <-> "NH2" Residue "A ARG 1076": "NH1" <-> "NH2" Residue "A ARG 1094": "NH1" <-> "NH2" Residue "A ARG 1121": "NH1" <-> "NH2" Residue "A ARG 1127": "NH1" <-> "NH2" Residue "A TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1200": "NH1" <-> "NH2" Residue "A ARG 1214": "NH1" <-> "NH2" Residue "A ARG 1272": "NH1" <-> "NH2" Residue "A ARG 1273": "NH1" <-> "NH2" Residue "A GLU 1364": "OE1" <-> "OE2" Residue "A GLU 1389": "OE1" <-> "OE2" Residue "A GLU 1448": "OE1" <-> "OE2" Residue "A GLU 1458": "OE1" <-> "OE2" Residue "A ARG 1481": "NH1" <-> "NH2" Residue "A GLU 1482": "OE1" <-> "OE2" Residue "A ARG 1489": "NH1" <-> "NH2" Residue "A ARG 1495": "NH1" <-> "NH2" Residue "A ARG 1500": "NH1" <-> "NH2" Residue "A GLU 1502": "OE1" <-> "OE2" Residue "A GLU 1518": "OE1" <-> "OE2" Residue "A ARG 1540": "NH1" <-> "NH2" Residue "A ARG 1545": "NH1" <-> "NH2" Residue "A GLU 1551": "OE1" <-> "OE2" Residue "A ARG 1556": "NH1" <-> "NH2" Residue "A GLU 1599": "OE1" <-> "OE2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B ARG 340": "NH1" <-> "NH2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B GLU 382": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12418 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 10442 Classifications: {'peptide': 1278} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 1232} Chain breaks: 5 Chain: "B" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1483 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 412 Unusual residues: {'NAG': 1, 'PC1': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PC1:plan-1': 2} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.87, per 1000 atoms: 0.55 Number of scatterers: 12418 At special positions: 0 Unit cell: (160.876, 108.7, 111.961, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 10 15.00 O 2162 8.00 N 1956 7.00 C 8194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 245 " distance=2.02 Simple disulfide: pdb=" SG CYS A1046 " - pdb=" SG CYS A1057 " distance=2.04 Simple disulfide: pdb=" SG CYS A1405 " - pdb=" SG CYS A1417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 313 " distance=2.04 Simple disulfide: pdb=" SG CYS B 246 " - pdb=" SG CYS B 261 " distance=2.04 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 341 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 377 " distance=2.03 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 361 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A1801 " - " ASN A 216 " " NAG B 501 " - " ASN B 217 " " NAG C 1 " - " ASN A1064 " " NAG D 1 " - " ASN A 210 " Time building additional restraints: 4.76 Conformation dependent library (CDL) restraints added in 2.5 seconds 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 5 sheets defined 65.1% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 36 through 55 removed outlier: 3.969A pdb=" N LEU A 41 " --> pdb=" O TRP A 37 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 65 through 91 removed outlier: 3.510A pdb=" N VAL A 70 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR A 71 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 74 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU A 77 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 80 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 83 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 85 " --> pdb=" O TYR A 82 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 87 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS A 89 " --> pdb=" O MET A 86 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 128 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 164 through 199 removed outlier: 3.562A pdb=" N GLN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 255 through 258 No H-bonds generated for 'chain 'A' and resid 255 through 258' Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 312 through 335 removed outlier: 3.794A pdb=" N VAL A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 380 removed outlier: 4.284A pdb=" N MET A 380 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 402 Processing helix chain 'A' and resid 420 through 440 Processing helix chain 'A' and resid 442 through 445 No H-bonds generated for 'chain 'A' and resid 442 through 445' Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.501A pdb=" N THR A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.701A pdb=" N TYR A 476 " --> pdb=" O GLN A 473 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU A 480 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 487 " --> pdb=" O ARG A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 500 Processing helix chain 'A' and resid 503 through 528 removed outlier: 3.620A pdb=" N SER A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 509 " --> pdb=" O LYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 Processing helix chain 'A' and resid 556 through 567 Processing helix chain 'A' and resid 569 through 588 Proline residue: A 573 - end of helix Processing helix chain 'A' and resid 590 through 602 Processing helix chain 'A' and resid 606 through 616 Processing helix chain 'A' and resid 847 through 854 Processing helix chain 'A' and resid 873 through 884 Processing helix chain 'A' and resid 887 through 905 removed outlier: 4.002A pdb=" N PHE A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 914 No H-bonds generated for 'chain 'A' and resid 912 through 914' Processing helix chain 'A' and resid 916 through 940 removed outlier: 4.893A pdb=" N ALA A 921 " --> pdb=" O THR A 917 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 922 " --> pdb=" O LEU A 918 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 926 " --> pdb=" O GLU A 922 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 971 Processing helix chain 'A' and resid 981 through 999 removed outlier: 3.997A pdb=" N CYS A 990 " --> pdb=" O MET A 986 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG A 992 " --> pdb=" O LEU A 988 " (cutoff:3.500A) Proline residue: A 993 - end of helix removed outlier: 4.614A pdb=" N ILE A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE A 997 " --> pdb=" O PRO A 993 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1039 removed outlier: 4.605A pdb=" N GLY A1013 " --> pdb=" O GLU A1009 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE A1014 " --> pdb=" O LEU A1010 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LYS A1015 " --> pdb=" O PHE A1011 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU A1016 " --> pdb=" O SER A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1056 No H-bonds generated for 'chain 'A' and resid 1054 through 1056' Processing helix chain 'A' and resid 1101 through 1113 removed outlier: 3.686A pdb=" N SER A1113 " --> pdb=" O PHE A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1127 Processing helix chain 'A' and resid 1131 through 1144 removed outlier: 3.624A pdb=" N VAL A1138 " --> pdb=" O TYR A1135 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A1139 " --> pdb=" O ILE A1136 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A1143 " --> pdb=" O VAL A1140 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N CYS A1144 " --> pdb=" O PHE A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1162 removed outlier: 4.083A pdb=" N PHE A1151 " --> pdb=" O GLY A1147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1152 " --> pdb=" O LEU A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1170 through 1184 Processing helix chain 'A' and resid 1198 through 1208 Processing helix chain 'A' and resid 1210 through 1227 removed outlier: 3.978A pdb=" N ARG A1214 " --> pdb=" O PRO A1210 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A1221 " --> pdb=" O ALA A1217 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU A1226 " --> pdb=" O ALA A1222 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU A1227 " --> pdb=" O GLN A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1262 Proline residue: A1240 - end of helix removed outlier: 3.720A pdb=" N ILE A1261 " --> pdb=" O MET A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1270 removed outlier: 3.845A pdb=" N GLN A1270 " --> pdb=" O ALA A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1294 Processing helix chain 'A' and resid 1297 through 1316 removed outlier: 4.107A pdb=" N SER A1313 " --> pdb=" O PHE A1309 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE A1314 " --> pdb=" O ARG A1310 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N CYS A1315 " --> pdb=" O PHE A1311 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY A1316 " --> pdb=" O PHE A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1334 Processing helix chain 'A' and resid 1336 through 1357 Processing helix chain 'A' and resid 1375 through 1387 Processing helix chain 'A' and resid 1391 through 1398 Processing helix chain 'A' and resid 1420 through 1435 removed outlier: 3.611A pdb=" N CYS A1428 " --> pdb=" O LEU A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1453 removed outlier: 4.189A pdb=" N LEU A1442 " --> pdb=" O MET A1438 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A1443 " --> pdb=" O LEU A1439 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER A1451 " --> pdb=" O VAL A1447 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1477 removed outlier: 3.681A pdb=" N VAL A1477 " --> pdb=" O ILE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1495 removed outlier: 4.207A pdb=" N LYS A1491 " --> pdb=" O THR A1487 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE A1492 " --> pdb=" O PHE A1488 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG A1495 " --> pdb=" O LYS A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1499 through 1501 No H-bonds generated for 'chain 'A' and resid 1499 through 1501' Processing helix chain 'A' and resid 1509 through 1522 removed outlier: 3.532A pdb=" N MET A1519 " --> pdb=" O MET A1515 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1539 Processing helix chain 'A' and resid 1544 through 1547 No H-bonds generated for 'chain 'A' and resid 1544 through 1547' Processing helix chain 'A' and resid 1550 through 1576 removed outlier: 3.985A pdb=" N LEU A1554 " --> pdb=" O LEU A1550 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A1555 " --> pdb=" O GLU A1551 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1601 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 262 through 287 removed outlier: 3.506A pdb=" N ASP B 272 " --> pdb=" O GLN B 269 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 275 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B 278 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 281 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER B 284 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 286 " --> pdb=" O GLU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 316 Processing helix chain 'B' and resid 330 through 340 removed outlier: 3.586A pdb=" N GLN B 338 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 207 through 209 Processing sheet with id= B, first strand: chain 'A' and resid 1044 through 1046 Processing sheet with id= C, first strand: chain 'A' and resid 1060 through 1064 Processing sheet with id= D, first strand: chain 'A' and resid 1484 through 1486 Processing sheet with id= E, first strand: chain 'B' and resid 327 through 329 631 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 5.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1861 1.28 - 1.41: 3408 1.41 - 1.55: 7233 1.55 - 1.69: 67 1.69 - 1.82: 150 Bond restraints: 12719 Sorted by residual: bond pdb=" C LEU A 78 " pdb=" N MET A 79 " ideal model delta sigma weight residual 1.335 1.245 0.090 1.30e-02 5.92e+03 4.83e+01 bond pdb=" C38 PC1 A1808 " pdb=" C39 PC1 A1808 " ideal model delta sigma weight residual 1.523 1.433 0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" N GLU B 373 " pdb=" CA GLU B 373 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.40e-03 1.83e+04 1.68e+01 bond pdb=" N VAL A 458 " pdb=" CA VAL A 458 " ideal model delta sigma weight residual 1.459 1.510 -0.051 1.30e-02 5.92e+03 1.54e+01 bond pdb=" C ARG A 992 " pdb=" O ARG A 992 " ideal model delta sigma weight residual 1.243 1.204 0.039 9.90e-03 1.02e+04 1.52e+01 ... (remaining 12714 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.71: 323 105.71 - 113.11: 6080 113.11 - 120.51: 6805 120.51 - 127.92: 3879 127.92 - 135.32: 93 Bond angle restraints: 17180 Sorted by residual: angle pdb=" N GLN A 414 " pdb=" CA GLN A 414 " pdb=" C GLN A 414 " ideal model delta sigma weight residual 112.93 99.84 13.09 1.33e+00 5.65e-01 9.69e+01 angle pdb=" N ASP B 372 " pdb=" CA ASP B 372 " pdb=" C ASP B 372 " ideal model delta sigma weight residual 111.28 103.22 8.06 1.09e+00 8.42e-01 5.47e+01 angle pdb=" N TYR A 419 " pdb=" CA TYR A 419 " pdb=" C TYR A 419 " ideal model delta sigma weight residual 113.55 105.76 7.79 1.26e+00 6.30e-01 3.82e+01 angle pdb=" CA ASP A 247 " pdb=" CB ASP A 247 " pdb=" CG ASP A 247 " ideal model delta sigma weight residual 112.60 118.21 -5.61 1.00e+00 1.00e+00 3.15e+01 angle pdb=" N PRO A 65 " pdb=" CA PRO A 65 " pdb=" C PRO A 65 " ideal model delta sigma weight residual 110.70 117.39 -6.69 1.22e+00 6.72e-01 3.00e+01 ... (remaining 17175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.60: 7008 19.60 - 39.21: 508 39.21 - 58.81: 143 58.81 - 78.41: 38 78.41 - 98.02: 9 Dihedral angle restraints: 7706 sinusoidal: 3412 harmonic: 4294 Sorted by residual: dihedral pdb=" CB CYS A1046 " pdb=" SG CYS A1046 " pdb=" SG CYS A1057 " pdb=" CB CYS A1057 " ideal model delta sinusoidal sigma weight residual -86.00 -155.69 69.69 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" CA CYS A 229 " pdb=" C CYS A 229 " pdb=" N SER A 230 " pdb=" CA SER A 230 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CB CYS B 324 " pdb=" SG CYS B 324 " pdb=" SG CYS B 377 " pdb=" CB CYS B 377 " ideal model delta sinusoidal sigma weight residual -86.00 -125.75 39.75 1 1.00e+01 1.00e-02 2.22e+01 ... (remaining 7703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 1809 0.182 - 0.365: 104 0.365 - 0.547: 0 0.547 - 0.729: 1 0.729 - 0.911: 1 Chirality restraints: 1915 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 210 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.49 -0.91 2.00e-01 2.50e+01 2.08e+01 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.30e+01 chirality pdb=" C1 NAG B 501 " pdb=" ND2 ASN B 217 " pdb=" C2 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.95 0.55 2.00e-01 2.50e+01 7.69e+00 ... (remaining 1912 not shown) Planarity restraints: 2082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.359 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG D 1 " 0.101 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.216 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.500 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.277 2.00e-02 2.50e+03 2.30e-01 6.61e+02 pdb=" C7 NAG D 2 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.384 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 217 " -0.081 2.00e-02 2.50e+03 1.16e-01 1.69e+02 pdb=" CG ASN B 217 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN B 217 " -0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN B 217 " 0.205 2.00e-02 2.50e+03 pdb=" C1 NAG B 501 " -0.130 2.00e-02 2.50e+03 ... (remaining 2079 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 334 2.74 - 3.28: 12427 3.28 - 3.82: 18870 3.82 - 4.36: 25221 4.36 - 4.90: 40235 Nonbonded interactions: 97087 Sorted by model distance: nonbonded pdb=" O3 NAG D 1 " pdb=" O7 NAG D 1 " model vdw 2.199 2.440 nonbonded pdb=" CE MET A 545 " pdb=" O22 PC1 A1805 " model vdw 2.224 3.460 nonbonded pdb=" NH1 ARG A 542 " pdb=" O14 PC1 A1805 " model vdw 2.225 2.520 nonbonded pdb=" O ASN A1072 " pdb=" ND2 ASN A1072 " model vdw 2.246 2.520 nonbonded pdb=" NH1 ARG A1273 " pdb=" C13 PC1 A1804 " model vdw 2.295 3.540 ... (remaining 97082 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 0.620 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: 0.010 Extract box with map and model: 3.210 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 35.090 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 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 : 0.015 0.090 12719 Z= 0.952 Angle : 1.770 13.090 17180 Z= 1.185 Chirality : 0.098 0.911 1915 Planarity : 0.014 0.295 2078 Dihedral : 15.850 98.016 4892 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.85 % Favored : 94.88 % Rotamer: Outliers : 2.12 % Allowed : 4.69 % Favored : 93.19 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.21), residues: 1444 helix: -0.05 (0.15), residues: 934 sheet: None (None), residues: 0 loop : -1.56 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.011 TRP B 311 HIS 0.013 0.003 HIS B 274 PHE 0.066 0.009 PHE A 997 TYR 0.081 0.009 TYR A 274 ARG 0.012 0.001 ARG A1481 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 329 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 8 residues processed: 348 average time/residue: 0.2688 time to fit residues: 130.0987 Evaluate side-chains 203 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 195 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 218 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 279 GLN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN A 451 HIS A 569 HIS A1072 ASN A1270 GLN A1460 GLN A1589 GLN ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN B 371 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12719 Z= 0.212 Angle : 0.644 8.485 17180 Z= 0.331 Chirality : 0.044 0.399 1915 Planarity : 0.005 0.035 2078 Dihedral : 13.667 70.235 2088 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.49 % Favored : 97.44 % Rotamer: Outliers : 3.03 % Allowed : 9.61 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1444 helix: 0.98 (0.17), residues: 929 sheet: None (None), residues: 0 loop : -1.29 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 107 HIS 0.004 0.001 HIS A 228 PHE 0.021 0.002 PHE A1530 TYR 0.014 0.001 TYR A1426 ARG 0.007 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 216 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: A 335 MET cc_start: 0.6379 (tmm) cc_final: 0.5601 (ttp) REVERT: A 381 MET cc_start: 0.3817 (mtp) cc_final: 0.3325 (mtt) outliers start: 40 outliers final: 26 residues processed: 241 average time/residue: 0.2298 time to fit residues: 80.4660 Evaluate side-chains 210 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 184 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1072 ASN Chi-restraints excluded: chain A residue 1209 HIS Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 303 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 404 ASN A1072 ASN A1460 GLN A1589 GLN B 227 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 12719 Z= 0.196 Angle : 0.575 7.317 17180 Z= 0.296 Chirality : 0.041 0.272 1915 Planarity : 0.004 0.038 2078 Dihedral : 12.408 72.929 2084 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.73 % Allowed : 10.98 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.22), residues: 1444 helix: 1.13 (0.17), residues: 934 sheet: -4.06 (1.15), residues: 10 loop : -1.22 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1117 HIS 0.003 0.001 HIS A 464 PHE 0.020 0.001 PHE A 389 TYR 0.014 0.001 TYR A1426 ARG 0.004 0.000 ARG A 951 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 201 time to evaluate : 1.499 Fit side-chains revert: symmetry clash REVERT: A 335 MET cc_start: 0.6442 (tmm) cc_final: 0.5682 (ttp) REVERT: A 381 MET cc_start: 0.3901 (mtp) cc_final: 0.3409 (mtt) outliers start: 36 outliers final: 26 residues processed: 219 average time/residue: 0.2360 time to fit residues: 76.0357 Evaluate side-chains 210 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 184 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 1209 HIS Chi-restraints excluded: chain A residue 1260 ILE Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 334 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 140 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 279 GLN A1419 ASN A1440 ASN A1589 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12719 Z= 0.203 Angle : 0.556 8.268 17180 Z= 0.286 Chirality : 0.040 0.227 1915 Planarity : 0.004 0.039 2078 Dihedral : 11.548 76.656 2082 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.26 % Allowed : 12.04 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.22), residues: 1444 helix: 1.21 (0.17), residues: 936 sheet: -4.19 (1.11), residues: 10 loop : -1.40 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1117 HIS 0.006 0.001 HIS A 228 PHE 0.017 0.001 PHE A1530 TYR 0.014 0.001 TYR A 415 ARG 0.007 0.000 ARG A1468 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 191 time to evaluate : 1.571 Fit side-chains revert: symmetry clash REVERT: A 335 MET cc_start: 0.6363 (tmm) cc_final: 0.5587 (ttp) REVERT: A 381 MET cc_start: 0.3803 (mtp) cc_final: 0.3294 (mtt) REVERT: B 216 TRP cc_start: 0.4415 (OUTLIER) cc_final: 0.2924 (t-100) REVERT: B 298 LYS cc_start: 0.8151 (mtpp) cc_final: 0.7846 (mttt) outliers start: 43 outliers final: 32 residues processed: 213 average time/residue: 0.2375 time to fit residues: 74.2333 Evaluate side-chains 216 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 183 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 1209 HIS Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1260 ILE Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1419 ASN Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1524 ASN Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 348 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1460 GLN A1589 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12719 Z= 0.253 Angle : 0.582 9.184 17180 Z= 0.296 Chirality : 0.047 0.951 1915 Planarity : 0.004 0.040 2078 Dihedral : 11.513 77.553 2080 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.41 % Allowed : 12.72 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1444 helix: 1.19 (0.17), residues: 934 sheet: -4.21 (1.07), residues: 10 loop : -1.51 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1117 HIS 0.004 0.001 HIS A 464 PHE 0.017 0.001 PHE A1488 TYR 0.014 0.001 TYR A 415 ARG 0.006 0.000 ARG A1468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 179 time to evaluate : 1.630 Fit side-chains revert: symmetry clash REVERT: A 335 MET cc_start: 0.6371 (tmm) cc_final: 0.5687 (ttp) REVERT: B 298 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7882 (mttt) outliers start: 45 outliers final: 37 residues processed: 205 average time/residue: 0.2234 time to fit residues: 68.1316 Evaluate side-chains 214 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 177 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 1209 HIS Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1296 ASN Chi-restraints excluded: chain A residue 1302 MET Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1524 ASN Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 379 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 116 optimal weight: 0.0570 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 73 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1460 GLN A1589 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12719 Z= 0.146 Angle : 0.525 7.387 17180 Z= 0.267 Chirality : 0.040 0.323 1915 Planarity : 0.004 0.039 2078 Dihedral : 10.911 77.512 2078 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.88 % Allowed : 13.70 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.23), residues: 1444 helix: 1.38 (0.17), residues: 927 sheet: -4.06 (1.19), residues: 10 loop : -1.44 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 216 HIS 0.003 0.001 HIS A1514 PHE 0.018 0.001 PHE A1488 TYR 0.015 0.001 TYR A 415 ARG 0.009 0.000 ARG A1468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 190 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.6359 (tmm) cc_final: 0.5700 (ttp) REVERT: B 216 TRP cc_start: 0.4340 (p-90) cc_final: 0.2991 (t-100) outliers start: 38 outliers final: 32 residues processed: 213 average time/residue: 0.2377 time to fit residues: 75.2644 Evaluate side-chains 210 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 178 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1209 HIS Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1302 MET Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 379 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 87 optimal weight: 0.0970 chunk 85 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1419 ASN A1460 GLN A1589 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12719 Z= 0.162 Angle : 0.540 12.029 17180 Z= 0.271 Chirality : 0.039 0.229 1915 Planarity : 0.004 0.038 2078 Dihedral : 10.648 76.321 2078 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.18 % Allowed : 14.08 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.22), residues: 1444 helix: 1.36 (0.17), residues: 935 sheet: -4.18 (1.22), residues: 10 loop : -1.52 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1413 HIS 0.007 0.001 HIS A1514 PHE 0.016 0.001 PHE A 389 TYR 0.022 0.001 TYR A 301 ARG 0.007 0.000 ARG A1468 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 187 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.6359 (tmm) cc_final: 0.5708 (ttp) outliers start: 42 outliers final: 35 residues processed: 212 average time/residue: 0.2494 time to fit residues: 78.7744 Evaluate side-chains 216 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1209 HIS Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1419 ASN Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 379 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 0.0770 chunk 83 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1460 GLN A1589 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12719 Z= 0.164 Angle : 0.547 11.105 17180 Z= 0.274 Chirality : 0.040 0.299 1915 Planarity : 0.004 0.038 2078 Dihedral : 10.521 75.036 2078 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.10 % Allowed : 14.76 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.23), residues: 1444 helix: 1.38 (0.17), residues: 935 sheet: -4.16 (1.23), residues: 10 loop : -1.51 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 216 HIS 0.004 0.001 HIS A1514 PHE 0.016 0.001 PHE A 849 TYR 0.017 0.001 TYR A 301 ARG 0.007 0.000 ARG A1468 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 183 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.6361 (tmm) cc_final: 0.5705 (ttp) outliers start: 41 outliers final: 36 residues processed: 209 average time/residue: 0.2210 time to fit residues: 69.6066 Evaluate side-chains 215 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 179 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1209 HIS Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1302 MET Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 379 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 2.9990 chunk 130 optimal weight: 0.0270 chunk 133 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 39 optimal weight: 0.0170 chunk 117 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1419 ASN A1440 ASN A1460 GLN A1589 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12719 Z= 0.149 Angle : 0.536 10.627 17180 Z= 0.270 Chirality : 0.039 0.227 1915 Planarity : 0.004 0.038 2078 Dihedral : 10.228 72.252 2074 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.80 % Allowed : 15.29 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.23), residues: 1444 helix: 1.40 (0.17), residues: 936 sheet: -4.18 (1.23), residues: 10 loop : -1.49 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 216 HIS 0.004 0.000 HIS A1514 PHE 0.011 0.001 PHE A1084 TYR 0.017 0.001 TYR A 301 ARG 0.008 0.000 ARG A1468 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 187 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.6362 (tmm) cc_final: 0.5721 (ttp) REVERT: A 1547 SER cc_start: 0.8067 (OUTLIER) cc_final: 0.7824 (t) REVERT: B 216 TRP cc_start: 0.4115 (p-90) cc_final: 0.3241 (t-100) outliers start: 37 outliers final: 33 residues processed: 210 average time/residue: 0.2211 time to fit residues: 70.1610 Evaluate side-chains 210 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1302 MET Chi-restraints excluded: chain A residue 1419 ASN Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain A residue 1589 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 379 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 144 optimal weight: 0.0170 chunk 132 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1460 GLN A1589 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12719 Z= 0.162 Angle : 0.546 11.807 17180 Z= 0.275 Chirality : 0.039 0.224 1915 Planarity : 0.004 0.038 2078 Dihedral : 10.177 70.684 2074 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.50 % Allowed : 15.67 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.23), residues: 1444 helix: 1.38 (0.17), residues: 940 sheet: -4.14 (1.23), residues: 10 loop : -1.50 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 216 HIS 0.003 0.001 HIS A1514 PHE 0.019 0.001 PHE A 849 TYR 0.017 0.001 TYR A 301 ARG 0.007 0.000 ARG A1468 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 179 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 MET cc_start: 0.6359 (tmm) cc_final: 0.5712 (ttp) REVERT: A 1536 MET cc_start: 0.6471 (ttp) cc_final: 0.6026 (ttp) REVERT: A 1547 SER cc_start: 0.8068 (OUTLIER) cc_final: 0.7825 (t) REVERT: B 216 TRP cc_start: 0.4129 (p-90) cc_final: 0.3304 (t-100) outliers start: 33 outliers final: 29 residues processed: 197 average time/residue: 0.2249 time to fit residues: 66.4975 Evaluate side-chains 207 residues out of total 1321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 177 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1302 MET Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 379 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 118 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.0470 chunk 101 optimal weight: 1.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1419 ASN A1460 GLN A1589 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.149989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.115639 restraints weight = 18582.343| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.38 r_work: 0.3360 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12719 Z= 0.144 Angle : 0.531 11.451 17180 Z= 0.267 Chirality : 0.038 0.224 1915 Planarity : 0.004 0.038 2078 Dihedral : 9.977 70.294 2074 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.50 % Allowed : 15.52 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1444 helix: 1.40 (0.17), residues: 941 sheet: -4.15 (1.23), residues: 10 loop : -1.50 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 216 HIS 0.002 0.000 HIS A1514 PHE 0.015 0.001 PHE A 72 TYR 0.015 0.001 TYR A 301 ARG 0.008 0.000 ARG A1468 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2783.99 seconds wall clock time: 51 minutes 8.06 seconds (3068.06 seconds total)