Starting phenix.real_space_refine on Tue May 20 01:07:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ayh_15713/05_2025/8ayh_15713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ayh_15713/05_2025/8ayh_15713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ayh_15713/05_2025/8ayh_15713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ayh_15713/05_2025/8ayh_15713.map" model { file = "/net/cci-nas-00/data/ceres_data/8ayh_15713/05_2025/8ayh_15713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ayh_15713/05_2025/8ayh_15713.cif" } resolution = 3.35 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= 0.001 sd= 0.007 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 Mg 1 5.21 5 S 75 5.16 5 C 12241 2.51 5 N 3167 2.21 5 O 3625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19109 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5123 Classifications: {'peptide': 648} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 613} Chain breaks: 1 Chain: "A" Number of atoms: 6454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6454 Classifications: {'peptide': 815} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 783} Chain breaks: 2 Chain: "B" Number of atoms: 7499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 951, 7499 Classifications: {'peptide': 951} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 901} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'H1H': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.95, per 1000 atoms: 0.52 Number of scatterers: 19109 At special positions: 0 Unit cell: (108.36, 145.34, 138.46, 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 75 16.00 Mg 1 11.99 O 3625 8.00 N 3167 7.00 C 12241 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS C 567 " - pdb=" SG CYS A 810 " distance=2.03 Simple disulfide: pdb=" SG CYS C 634 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 698 " - pdb=" SG CYS A 724 " distance=2.03 Simple disulfide: pdb=" SG CYS A 699 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 711 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A 856 " - pdb=" SG CYS A 883 " distance=2.04 Simple disulfide: pdb=" SG CYS A1101 " - pdb=" SG CYS A1159 " distance=2.03 Simple disulfide: pdb=" SG CYS A1375 " - pdb=" SG CYS A1505 " distance=2.04 Simple disulfide: pdb=" SG CYS A1405 " - pdb=" SG CYS A1474 " distance=2.04 Simple disulfide: pdb=" SG CYS B 544 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS B 609 " - pdb=" SG CYS B 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B1340 " - pdb=" SG CYS B1468 " distance=2.03 Simple disulfide: pdb=" SG CYS B1368 " - pdb=" SG CYS B1437 " distance=2.03 Simple disulfide: pdb=" SG CYS B1485 " - pdb=" SG CYS B1490 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 4.33 Conformation dependent library (CDL) restraints added in 2.4 seconds 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4550 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 53 sheets defined 14.1% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.672A pdb=" N LEU C 92 " --> pdb=" O PRO C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 removed outlier: 3.582A pdb=" N ALA C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 496 Processing helix chain 'C' and resid 608 through 610 No H-bonds generated for 'chain 'C' and resid 608 through 610' Processing helix chain 'C' and resid 623 through 628 Processing helix chain 'C' and resid 629 through 631 No H-bonds generated for 'chain 'C' and resid 629 through 631' Processing helix chain 'C' and resid 641 through 649 removed outlier: 3.595A pdb=" N VAL C 645 " --> pdb=" O ASN C 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 689 removed outlier: 3.946A pdb=" N GLU A 685 " --> pdb=" O LYS A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 701 Processing helix chain 'A' and resid 721 through 737 removed outlier: 3.612A pdb=" N CYS A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL A 734 " --> pdb=" O GLU A 730 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 743 through 754 removed outlier: 3.770A pdb=" N LEU A 749 " --> pdb=" O LYS A 745 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 752 " --> pdb=" O GLN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 758 Processing helix chain 'A' and resid 984 through 992 removed outlier: 3.580A pdb=" N ALA A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1013 Processing helix chain 'A' and resid 1015 through 1028 removed outlier: 3.534A pdb=" N VAL A1021 " --> pdb=" O PRO A1017 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR A1024 " --> pdb=" O TYR A1020 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A1026 " --> pdb=" O PHE A1022 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A1027 " --> pdb=" O HIS A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1055 removed outlier: 3.574A pdb=" N GLN A1043 " --> pdb=" O LEU A1039 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A1048 " --> pdb=" O LYS A1044 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET A1053 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A1054 " --> pdb=" O LYS A1050 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A1055 " --> pdb=" O GLU A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1090 removed outlier: 3.549A pdb=" N GLN A1088 " --> pdb=" O ARG A1084 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1111 removed outlier: 3.855A pdb=" N ILE A1100 " --> pdb=" O ASN A1096 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A1107 " --> pdb=" O SER A1103 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A1108 " --> pdb=" O LEU A1104 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A1109 " --> pdb=" O LEU A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1154 removed outlier: 3.973A pdb=" N ARG A1138 " --> pdb=" O PRO A1134 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A1150 " --> pdb=" O ALA A1146 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A1151 " --> pdb=" O PHE A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1178 removed outlier: 3.896A pdb=" N ASP A1165 " --> pdb=" O LEU A1161 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A1169 " --> pdb=" O ASP A1165 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS A1170 " --> pdb=" O THR A1166 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A1178 " --> pdb=" O PHE A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1195 Processing helix chain 'A' and resid 1204 through 1215 removed outlier: 3.909A pdb=" N GLU A1215 " --> pdb=" O ALA A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1261 Processing helix chain 'A' and resid 1263 through 1278 removed outlier: 3.993A pdb=" N VAL A1267 " --> pdb=" O ASP A1263 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A1268 " --> pdb=" O ILE A1264 " (cutoff:3.500A) Proline residue: A1269 - end of helix removed outlier: 3.704A pdb=" N LYS A1272 " --> pdb=" O ASN A1268 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A1276 " --> pdb=" O LYS A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1295 removed outlier: 3.759A pdb=" N ASN A1292 " --> pdb=" O GLN A1288 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA A1293 " --> pdb=" O ASP A1289 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU A1295 " --> pdb=" O ILE A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1441 removed outlier: 3.637A pdb=" N LEU A1439 " --> pdb=" O ASN A1435 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 301 Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 421 through 425 removed outlier: 3.847A pdb=" N GLN B 425 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.908A pdb=" N ILE B 476 " --> pdb=" O LEU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 515 removed outlier: 3.825A pdb=" N ILE B 515 " --> pdb=" O PRO B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 586 Processing helix chain 'B' and resid 594 through 603 removed outlier: 3.682A pdb=" N THR B 601 " --> pdb=" O LYS B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 623 removed outlier: 3.976A pdb=" N PHE B 621 " --> pdb=" O ASN B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 1396 through 1401 Processing sheet with id=AA1, first strand: chain 'C' and resid 80 through 85 removed outlier: 8.521A pdb=" N ASN C 38 " --> pdb=" O PRO C 28 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 25 " --> pdb=" O LEU C 654 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 654 " --> pdb=" O ILE C 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 31 through 32 removed outlier: 6.446A pdb=" N PHE C 31 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER C 67 " --> pdb=" O ILE C 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 31 through 32 removed outlier: 6.446A pdb=" N PHE C 31 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 125 through 130 Processing sheet with id=AA5, first strand: chain 'C' and resid 134 through 135 removed outlier: 3.593A pdb=" N PHE C 217 " --> pdb=" O TRP C 199 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS C 204 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP C 172 " --> pdb=" O PHE C 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AA7, first strand: chain 'C' and resid 221 through 222 removed outlier: 6.022A pdb=" N GLU C 221 " --> pdb=" O ILE A 765 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 228 through 233 Processing sheet with id=AA9, first strand: chain 'C' and resid 237 through 238 Processing sheet with id=AB1, first strand: chain 'C' and resid 281 through 282 removed outlier: 3.538A pdb=" N ALA C 263 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 267 " --> pdb=" O GLN C 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 281 through 282 removed outlier: 3.550A pdb=" N ILE C 325 " --> pdb=" O ILE C 342 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AB4, first strand: chain 'C' and resid 362 through 363 removed outlier: 7.376A pdb=" N THR C 429 " --> pdb=" O ALA C 456 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 407 through 410 Processing sheet with id=AB6, first strand: chain 'C' and resid 465 through 469 Processing sheet with id=AB7, first strand: chain 'C' and resid 508 through 516 removed outlier: 5.291A pdb=" N ILE C 509 " --> pdb=" O SER C 505 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER C 505 " --> pdb=" O ILE C 509 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N HIS C 498 " --> pdb=" O ILE C 545 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE C 545 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER C 538 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 553 " --> pdb=" O VAL C 546 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 572 through 576 Processing sheet with id=AB9, first strand: chain 'A' and resid 776 through 781 removed outlier: 3.580A pdb=" N GLU A 776 " --> pdb=" O LEU C 602 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 598 " --> pdb=" O VAL A 780 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 776 through 781 removed outlier: 3.580A pdb=" N GLU A 776 " --> pdb=" O LEU C 602 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 598 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TRP A 797 " --> pdb=" O ALA A 817 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 823 through 827 Processing sheet with id=AC3, first strand: chain 'A' and resid 833 through 834 removed outlier: 6.134A pdb=" N VAL A 833 " --> pdb=" O VAL A 930 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 838 through 839 Processing sheet with id=AC5, first strand: chain 'A' and resid 853 through 855 Processing sheet with id=AC6, first strand: chain 'A' and resid 857 through 859 removed outlier: 3.725A pdb=" N LYS A 858 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 919 " --> pdb=" O THR A 916 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 935 through 944 removed outlier: 3.559A pdb=" N LYS A 974 " --> pdb=" O VAL A1364 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG A 975 " --> pdb=" O VAL A1340 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 956 through 959 removed outlier: 3.860A pdb=" N LYS A 957 " --> pdb=" O VAL A1348 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1217 through 1219 removed outlier: 3.665A pdb=" N TYR A1225 " --> pdb=" O LYS A1219 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1377 through 1385 removed outlier: 3.569A pdb=" N LYS A1380 " --> pdb=" O CYS A1405 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS A1400 " --> pdb=" O ILE A1479 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A1477 " --> pdb=" O ILE A1402 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1452 through 1456 removed outlier: 3.715A pdb=" N ASP A1452 " --> pdb=" O GLN A1463 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR A1492 " --> pdb=" O SER A1427 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 24 through 28 Processing sheet with id=AD4, first strand: chain 'B' and resid 32 through 33 removed outlier: 3.533A pdb=" N VAL B 113 " --> pdb=" O GLY B 110 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 69 " --> pdb=" O VAL B 58 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 39 through 40 Processing sheet with id=AD6, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AD7, first strand: chain 'B' and resid 136 through 137 removed outlier: 3.588A pdb=" N PHE B 214 " --> pdb=" O TRP B 197 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 161 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 165 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 174 " --> pdb=" O PHE B 165 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 224 through 230 Processing sheet with id=AD9, first strand: chain 'B' and resid 234 through 236 removed outlier: 5.075A pdb=" N PHE B 235 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 336 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY B 266 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 273 through 275 removed outlier: 3.553A pdb=" N GLY B 266 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 344 through 346 Processing sheet with id=AE3, first strand: chain 'B' and resid 380 through 381 removed outlier: 3.588A pdb=" N SER B 386 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 408 through 414 Processing sheet with id=AE5, first strand: chain 'B' and resid 444 through 448 removed outlier: 3.814A pdb=" N LYS B 467 " --> pdb=" O TYR B 444 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 488 through 496 removed outlier: 5.199A pdb=" N ILE B 489 " --> pdb=" O ASN B 485 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN B 485 " --> pdb=" O ILE B 489 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 491 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR B 481 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR B 478 " --> pdb=" O GLN B 525 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLN B 525 " --> pdb=" O TYR B 478 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 488 through 496 removed outlier: 5.199A pdb=" N ILE B 489 " --> pdb=" O ASN B 485 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN B 485 " --> pdb=" O ILE B 489 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 491 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR B 481 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR B 478 " --> pdb=" O GLN B 525 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLN B 525 " --> pdb=" O TYR B 478 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 548 through 551 Processing sheet with id=AE9, first strand: chain 'B' and resid 556 through 557 Processing sheet with id=AF1, first strand: chain 'B' and resid 574 through 576 Processing sheet with id=AF2, first strand: chain 'B' and resid 792 through 795 removed outlier: 3.647A pdb=" N CYS B 801 " --> pdb=" O SER B 793 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 814 through 817 removed outlier: 3.560A pdb=" N SER B 876 " --> pdb=" O ASN B 838 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 824 through 825 removed outlier: 3.525A pdb=" N LYS B 911 " --> pdb=" O VAL B 894 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 866 " --> pdb=" O LEU B 850 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 1343 through 1350 removed outlier: 3.697A pdb=" N ASN B1346 " --> pdb=" O CYS B1368 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS B1368 " --> pdb=" O ASN B1346 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B1363 " --> pdb=" O ILE B1442 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B1442 " --> pdb=" O LEU B1363 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 1406 through 1407 removed outlier: 6.382A pdb=" N LYS B1429 " --> pdb=" O THR B1378 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR B1378 " --> pdb=" O LYS B1429 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N CYS B1468 " --> pdb=" O VAL B1458 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 1413 through 1414 Processing sheet with id=AF8, first strand: chain 'B' and resid 1483 through 1486 removed outlier: 3.553A pdb=" N ARG B1491 " --> pdb=" O ILE B1484 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B1489 " --> pdb=" O ILE B1486 " (cutoff:3.500A) 685 hydrogen bonds defined for protein. 1842 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: 11.02 Time building geometry restraints manager: 5.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6062 1.34 - 1.46: 4325 1.46 - 1.58: 9022 1.58 - 1.70: 0 1.70 - 1.82: 118 Bond restraints: 19527 Sorted by residual: bond pdb=" C30 H1H A1701 " pdb=" O32 H1H A1701 " ideal model delta sigma weight residual 1.240 1.337 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C1 H1H A1701 " pdb=" O7 H1H A1701 " ideal model delta sigma weight residual 1.345 1.395 -0.050 2.00e-02 2.50e+03 6.36e+00 bond pdb=" C23 H1H A1701 " pdb=" O28 H1H A1701 " ideal model delta sigma weight residual 1.350 1.398 -0.048 2.00e-02 2.50e+03 5.88e+00 bond pdb=" C ASN C 423 " pdb=" N LEU C 424 " ideal model delta sigma weight residual 1.331 1.266 0.065 2.83e-02 1.25e+03 5.20e+00 bond pdb=" C LEU B 221 " pdb=" N PRO B 222 " ideal model delta sigma weight residual 1.335 1.314 0.021 9.40e-03 1.13e+04 5.00e+00 ... (remaining 19522 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 25840 2.47 - 4.95: 573 4.95 - 7.42: 71 7.42 - 9.90: 18 9.90 - 12.37: 4 Bond angle restraints: 26506 Sorted by residual: angle pdb=" N SER C 311 " pdb=" CA SER C 311 " pdb=" C SER C 311 " ideal model delta sigma weight residual 111.37 119.11 -7.74 1.64e+00 3.72e-01 2.23e+01 angle pdb=" C PHE C 518 " pdb=" N SER C 519 " pdb=" CA SER C 519 " ideal model delta sigma weight residual 120.38 126.06 -5.68 1.37e+00 5.33e-01 1.72e+01 angle pdb=" C ARG A 766 " pdb=" N SER A 767 " pdb=" CA SER A 767 " ideal model delta sigma weight residual 122.19 131.42 -9.23 2.30e+00 1.89e-01 1.61e+01 angle pdb=" C THR A1132 " pdb=" N LEU A1133 " pdb=" CA LEU A1133 " ideal model delta sigma weight residual 120.09 125.09 -5.00 1.25e+00 6.40e-01 1.60e+01 angle pdb=" CA THR A1242 " pdb=" CB THR A1242 " pdb=" CG2 THR A1242 " ideal model delta sigma weight residual 110.50 117.30 -6.80 1.70e+00 3.46e-01 1.60e+01 ... (remaining 26501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 10502 17.71 - 35.41: 1061 35.41 - 53.12: 184 53.12 - 70.82: 26 70.82 - 88.53: 13 Dihedral angle restraints: 11786 sinusoidal: 4718 harmonic: 7068 Sorted by residual: dihedral pdb=" CB CYS A 711 " pdb=" SG CYS A 711 " pdb=" SG CYS A 732 " pdb=" CB CYS A 732 " ideal model delta sinusoidal sigma weight residual 93.00 177.85 -84.85 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CA LEU C 310 " pdb=" C LEU C 310 " pdb=" N SER C 311 " pdb=" CA SER C 311 " ideal model delta harmonic sigma weight residual -180.00 -142.55 -37.45 0 5.00e+00 4.00e-02 5.61e+01 dihedral pdb=" CB CYS C 634 " pdb=" SG CYS C 634 " pdb=" SG CYS C 669 " pdb=" CB CYS C 669 " ideal model delta sinusoidal sigma weight residual -86.00 -141.06 55.06 1 1.00e+01 1.00e-02 4.10e+01 ... (remaining 11783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2117 0.051 - 0.103: 672 0.103 - 0.154: 206 0.154 - 0.206: 20 0.206 - 0.257: 9 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CG LEU B 400 " pdb=" CB LEU B 400 " pdb=" CD1 LEU B 400 " pdb=" CD2 LEU B 400 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL B 192 " pdb=" CA VAL B 192 " pdb=" CG1 VAL B 192 " pdb=" CG2 VAL B 192 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL B 584 " pdb=" CA VAL B 584 " pdb=" CG1 VAL B 584 " pdb=" CG2 VAL B 584 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 3021 not shown) Planarity restraints: 3374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 165 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO C 166 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 166 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 166 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 511 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO B 512 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 512 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 512 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 358 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO B 359 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 359 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 359 " 0.033 5.00e-02 4.00e+02 ... (remaining 3371 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 432 2.67 - 3.23: 16192 3.23 - 3.79: 28764 3.79 - 4.34: 38665 4.34 - 4.90: 65784 Nonbonded interactions: 149837 Sorted by model distance: nonbonded pdb=" OD1 ASP B 542 " pdb="MG MG B2000 " model vdw 2.114 2.170 nonbonded pdb=" OD1 ASP B 539 " pdb="MG MG B2000 " model vdw 2.143 2.170 nonbonded pdb=" OD1 ASN A1268 " pdb=" OH TYR A1300 " model vdw 2.269 3.040 nonbonded pdb=" O PRO B 351 " pdb=" OH TYR B 360 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR C 655 " pdb=" O ASN C 658 " model vdw 2.283 3.040 ... (remaining 149832 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.340 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: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 47.860 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 : 0.007 0.119 19541 Z= 0.317 Angle : 0.913 12.373 26534 Z= 0.499 Chirality : 0.056 0.257 3024 Planarity : 0.007 0.072 3374 Dihedral : 14.462 88.529 7194 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.47 % Favored : 93.45 % Rotamer: Outliers : 0.65 % Allowed : 10.31 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.12 (0.14), residues: 2396 helix: -4.60 (0.11), residues: 316 sheet: -2.07 (0.15), residues: 925 loop : -2.68 (0.15), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 917 HIS 0.006 0.001 HIS A1421 PHE 0.024 0.003 PHE C 217 TYR 0.030 0.002 TYR C 240 ARG 0.007 0.001 ARG A 717 Details of bonding type rmsd hydrogen bonds : bond 0.26682 ( 640) hydrogen bonds : angle 9.76940 ( 1842) SS BOND : bond 0.00290 ( 14) SS BOND : angle 1.53240 ( 28) covalent geometry : bond 0.00739 (19527) covalent geometry : angle 0.91181 (26506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 286 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 193 ASN cc_start: 0.8270 (t0) cc_final: 0.8038 (t0) REVERT: A 804 ILE cc_start: 0.9317 (mm) cc_final: 0.9113 (mm) REVERT: A 1024 TYR cc_start: 0.7459 (t80) cc_final: 0.7180 (t80) REVERT: B 107 GLN cc_start: 0.7378 (tt0) cc_final: 0.6890 (mt0) REVERT: B 771 ILE cc_start: 0.9326 (mm) cc_final: 0.9084 (mt) outliers start: 14 outliers final: 9 residues processed: 299 average time/residue: 0.3229 time to fit residues: 145.3574 Evaluate side-chains 185 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 885 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 217 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 GLN C 399 GLN C 533 ASN C 644 ASN C 658 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 GLN A1292 ASN A1463 GLN B 112 GLN B 187 ASN B 405 ASN B 416 ASN B 465 ASN B 501 GLN B 507 ASN B 557 GLN B 638 GLN B 869 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.097993 restraints weight = 34782.922| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.48 r_work: 0.3038 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19541 Z= 0.143 Angle : 0.594 10.334 26534 Z= 0.311 Chirality : 0.046 0.198 3024 Planarity : 0.005 0.053 3374 Dihedral : 5.783 44.616 2630 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.01 % Allowed : 14.04 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.15), residues: 2396 helix: -3.01 (0.21), residues: 321 sheet: -1.37 (0.16), residues: 929 loop : -2.22 (0.16), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1106 HIS 0.003 0.001 HIS B1445 PHE 0.025 0.001 PHE A 820 TYR 0.014 0.001 TYR A1092 ARG 0.004 0.000 ARG A 766 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 640) hydrogen bonds : angle 6.16289 ( 1842) SS BOND : bond 0.00694 ( 14) SS BOND : angle 1.27942 ( 28) covalent geometry : bond 0.00329 (19527) covalent geometry : angle 0.59257 (26506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 193 ASN cc_start: 0.8263 (t0) cc_final: 0.8034 (t0) REVERT: C 276 LYS cc_start: 0.8371 (mmmt) cc_final: 0.7891 (mptt) REVERT: C 339 GLU cc_start: 0.8103 (mp0) cc_final: 0.7837 (mp0) REVERT: A 804 ILE cc_start: 0.9158 (mm) cc_final: 0.8905 (mm) REVERT: A 1024 TYR cc_start: 0.7678 (t80) cc_final: 0.7407 (t80) REVERT: A 1247 MET cc_start: 0.8236 (ttm) cc_final: 0.7991 (ttm) REVERT: B 453 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7828 (tm-30) outliers start: 43 outliers final: 30 residues processed: 257 average time/residue: 0.2938 time to fit residues: 119.2423 Evaluate side-chains 216 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 644 ASN Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1014 SER Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 1482 ASN Chi-restraints excluded: chain B residue 1485 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 225 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 235 optimal weight: 9.9990 chunk 79 optimal weight: 0.0970 chunk 105 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 164 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 446 ASN ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 GLN A1360 HIS B 65 GLN ** B 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1346 ASN B1419 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.098909 restraints weight = 34894.465| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.50 r_work: 0.3064 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19541 Z= 0.125 Angle : 0.548 10.208 26534 Z= 0.283 Chirality : 0.045 0.168 3024 Planarity : 0.004 0.050 3374 Dihedral : 5.292 47.228 2628 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.18 % Favored : 94.78 % Rotamer: Outliers : 2.61 % Allowed : 15.21 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.16), residues: 2396 helix: -2.23 (0.24), residues: 325 sheet: -0.92 (0.16), residues: 951 loop : -1.96 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1106 HIS 0.005 0.001 HIS C 226 PHE 0.015 0.001 PHE A 820 TYR 0.011 0.001 TYR A 950 ARG 0.003 0.000 ARG A 766 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 640) hydrogen bonds : angle 5.44747 ( 1842) SS BOND : bond 0.00278 ( 14) SS BOND : angle 1.05157 ( 28) covalent geometry : bond 0.00295 (19527) covalent geometry : angle 0.54762 (26506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 175 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: A 804 ILE cc_start: 0.9047 (mm) cc_final: 0.8755 (mm) REVERT: A 917 TRP cc_start: 0.7495 (t-100) cc_final: 0.7061 (m100) REVERT: A 1024 TYR cc_start: 0.7672 (t80) cc_final: 0.7439 (t80) REVERT: A 1044 LYS cc_start: 0.6939 (mmmt) cc_final: 0.6641 (tttm) REVERT: A 1057 MET cc_start: 0.7745 (tpp) cc_final: 0.7463 (ttm) REVERT: B 107 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7679 (mt0) REVERT: B 264 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8506 (tt) REVERT: B 453 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7753 (tm-30) outliers start: 56 outliers final: 41 residues processed: 254 average time/residue: 0.2915 time to fit residues: 117.2907 Evaluate side-chains 227 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 838 ASN Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 1346 ASN Chi-restraints excluded: chain B residue 1378 THR Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1482 ASN Chi-restraints excluded: chain B residue 1485 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 117 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 136 optimal weight: 8.9990 chunk 20 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 95 optimal weight: 0.0070 chunk 226 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN C 644 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 GLN A1090 ASN A1178 ASN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.122975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.100508 restraints weight = 34904.222| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.42 r_work: 0.3099 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 19541 Z= 0.099 Angle : 0.516 9.167 26534 Z= 0.266 Chirality : 0.045 0.150 3024 Planarity : 0.004 0.050 3374 Dihedral : 4.991 51.834 2628 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.61 % Allowed : 16.28 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.16), residues: 2396 helix: -1.47 (0.27), residues: 327 sheet: -0.49 (0.17), residues: 924 loop : -1.81 (0.17), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1106 HIS 0.005 0.001 HIS A1202 PHE 0.014 0.001 PHE B 224 TYR 0.024 0.001 TYR B1411 ARG 0.003 0.000 ARG B 865 Details of bonding type rmsd hydrogen bonds : bond 0.02946 ( 640) hydrogen bonds : angle 5.05323 ( 1842) SS BOND : bond 0.00277 ( 14) SS BOND : angle 1.19145 ( 28) covalent geometry : bond 0.00231 (19527) covalent geometry : angle 0.51519 (26506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 175 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: C 253 ARG cc_start: 0.7704 (ptp-110) cc_final: 0.7353 (ptt90) REVERT: C 276 LYS cc_start: 0.8431 (mmmt) cc_final: 0.7927 (mptt) REVERT: C 554 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8977 (mt) REVERT: A 804 ILE cc_start: 0.9012 (mm) cc_final: 0.8686 (mm) REVERT: A 825 LEU cc_start: 0.8331 (pt) cc_final: 0.8096 (tp) REVERT: A 826 GLU cc_start: 0.8445 (pm20) cc_final: 0.7815 (pm20) REVERT: A 917 TRP cc_start: 0.7817 (t-100) cc_final: 0.7357 (m100) REVERT: A 1005 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7931 (mmmt) REVERT: A 1024 TYR cc_start: 0.7787 (t80) cc_final: 0.7561 (t80) REVERT: A 1092 TYR cc_start: 0.7498 (m-80) cc_final: 0.7141 (m-10) REVERT: A 1158 ILE cc_start: 0.8615 (mt) cc_final: 0.8400 (mt) REVERT: A 1161 LEU cc_start: 0.8639 (mm) cc_final: 0.7875 (tt) REVERT: A 1206 ARG cc_start: 0.7707 (tpp80) cc_final: 0.7495 (tpp-160) REVERT: A 1247 MET cc_start: 0.8314 (ttm) cc_final: 0.8106 (ttm) REVERT: B 453 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7980 (tm-30) REVERT: B 1464 LEU cc_start: 0.8544 (mm) cc_final: 0.8267 (mt) REVERT: B 1475 ASP cc_start: 0.8418 (p0) cc_final: 0.8214 (p0) outliers start: 56 outliers final: 38 residues processed: 255 average time/residue: 0.2826 time to fit residues: 113.9341 Evaluate side-chains 226 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 838 ASN Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 1378 THR Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1485 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 115 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 96 optimal weight: 0.3980 chunk 59 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 182 optimal weight: 0.4980 chunk 220 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 GLN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.120444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.097968 restraints weight = 35009.642| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.43 r_work: 0.3041 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 19541 Z= 0.154 Angle : 0.553 10.417 26534 Z= 0.281 Chirality : 0.046 0.167 3024 Planarity : 0.004 0.049 3374 Dihedral : 5.080 56.761 2628 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.34 % Favored : 94.62 % Rotamer: Outliers : 3.17 % Allowed : 16.51 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.17), residues: 2396 helix: -1.19 (0.27), residues: 328 sheet: -0.39 (0.17), residues: 957 loop : -1.72 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1106 HIS 0.005 0.001 HIS C 226 PHE 0.012 0.001 PHE C 217 TYR 0.020 0.001 TYR B1411 ARG 0.005 0.000 ARG A 947 Details of bonding type rmsd hydrogen bonds : bond 0.03099 ( 640) hydrogen bonds : angle 5.01242 ( 1842) SS BOND : bond 0.00260 ( 14) SS BOND : angle 1.05282 ( 28) covalent geometry : bond 0.00370 (19527) covalent geometry : angle 0.55263 (26506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 190 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 175 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: C 253 ARG cc_start: 0.7617 (ptp-110) cc_final: 0.7393 (ptt90) REVERT: C 276 LYS cc_start: 0.8419 (mmmt) cc_final: 0.7946 (mptt) REVERT: C 554 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8932 (mt) REVERT: A 804 ILE cc_start: 0.9011 (mm) cc_final: 0.8682 (mm) REVERT: A 826 GLU cc_start: 0.8299 (pm20) cc_final: 0.7664 (pm20) REVERT: A 917 TRP cc_start: 0.7544 (t-100) cc_final: 0.7291 (m100) REVERT: A 1005 LYS cc_start: 0.8337 (mtpt) cc_final: 0.7972 (mmmm) REVERT: A 1024 TYR cc_start: 0.7753 (t80) cc_final: 0.7544 (t80) REVERT: A 1044 LYS cc_start: 0.7029 (mmmt) cc_final: 0.6719 (tttm) REVERT: A 1158 ILE cc_start: 0.8652 (mt) cc_final: 0.8428 (mt) REVERT: A 1161 LEU cc_start: 0.8574 (mm) cc_final: 0.7799 (tt) REVERT: A 1247 MET cc_start: 0.8272 (ttm) cc_final: 0.8043 (ttm) REVERT: B 107 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7515 (mt0) REVERT: B 264 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8570 (tp) REVERT: B 350 THR cc_start: 0.8944 (t) cc_final: 0.8716 (t) REVERT: B 453 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7800 (tm-30) REVERT: B 1467 LYS cc_start: 0.8008 (mmmm) cc_final: 0.7726 (mmmt) outliers start: 68 outliers final: 52 residues processed: 246 average time/residue: 0.3015 time to fit residues: 116.0484 Evaluate side-chains 240 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1014 SER Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 838 ASN Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 1378 THR Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1485 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 112 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 656 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 GLN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1452 GLN ** B1473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.118621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.096224 restraints weight = 34829.631| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.46 r_work: 0.3015 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 19541 Z= 0.198 Angle : 0.585 11.495 26534 Z= 0.298 Chirality : 0.046 0.160 3024 Planarity : 0.004 0.048 3374 Dihedral : 5.280 57.887 2628 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.14 % Favored : 93.82 % Rotamer: Outliers : 4.15 % Allowed : 16.18 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.17), residues: 2396 helix: -1.01 (0.27), residues: 327 sheet: -0.38 (0.17), residues: 954 loop : -1.62 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1106 HIS 0.006 0.001 HIS C 226 PHE 0.016 0.002 PHE B 464 TYR 0.017 0.001 TYR C 457 ARG 0.003 0.000 ARG A1153 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 640) hydrogen bonds : angle 5.09121 ( 1842) SS BOND : bond 0.00278 ( 14) SS BOND : angle 1.07147 ( 28) covalent geometry : bond 0.00476 (19527) covalent geometry : angle 0.58454 (26506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 189 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 253 ARG cc_start: 0.7670 (ptp-110) cc_final: 0.7441 (ptt90) REVERT: C 276 LYS cc_start: 0.8447 (mmmt) cc_final: 0.7978 (mptt) REVERT: C 444 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7676 (tm-30) REVERT: C 554 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8959 (mt) REVERT: A 796 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8668 (p) REVERT: A 804 ILE cc_start: 0.9072 (mm) cc_final: 0.8787 (mm) REVERT: A 826 GLU cc_start: 0.8346 (pm20) cc_final: 0.7580 (pm20) REVERT: A 917 TRP cc_start: 0.7583 (t-100) cc_final: 0.7244 (m100) REVERT: A 988 LEU cc_start: 0.8855 (mm) cc_final: 0.8583 (mp) REVERT: A 1024 TYR cc_start: 0.7862 (t80) cc_final: 0.7634 (t80) REVERT: A 1044 LYS cc_start: 0.7032 (mmmt) cc_final: 0.6713 (tttm) REVERT: A 1158 ILE cc_start: 0.8658 (mt) cc_final: 0.8403 (mt) REVERT: A 1161 LEU cc_start: 0.8540 (mm) cc_final: 0.7737 (tt) REVERT: A 1247 MET cc_start: 0.8240 (ttm) cc_final: 0.7899 (ttm) REVERT: B 107 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7565 (mt0) REVERT: B 183 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.6810 (p90) REVERT: B 264 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8527 (tt) REVERT: B 321 MET cc_start: 0.8362 (mtt) cc_final: 0.8049 (mtt) REVERT: B 350 THR cc_start: 0.9031 (t) cc_final: 0.8829 (t) REVERT: B 453 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7784 (tm-30) REVERT: B 811 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.6984 (tpt) REVERT: B 1467 LYS cc_start: 0.8013 (mmmm) cc_final: 0.7762 (mmmt) REVERT: B 1481 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7331 (pp) outliers start: 89 outliers final: 58 residues processed: 263 average time/residue: 0.2762 time to fit residues: 116.2774 Evaluate side-chains 243 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 178 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1341 LEU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1489 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 811 MET Chi-restraints excluded: chain B residue 838 ASN Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 1378 THR Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1480 LEU Chi-restraints excluded: chain B residue 1481 LEU Chi-restraints excluded: chain B residue 1485 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 28 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 ASN ** B1473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.118150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.096005 restraints weight = 34619.207| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.35 r_work: 0.2999 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 19541 Z= 0.245 Angle : 0.622 12.549 26534 Z= 0.317 Chirality : 0.048 0.174 3024 Planarity : 0.004 0.047 3374 Dihedral : 5.493 53.385 2628 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.84 % Favored : 93.11 % Rotamer: Outliers : 3.82 % Allowed : 17.54 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.17), residues: 2396 helix: -1.01 (0.27), residues: 329 sheet: -0.41 (0.17), residues: 949 loop : -1.60 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1106 HIS 0.007 0.001 HIS C 226 PHE 0.017 0.002 PHE B 464 TYR 0.024 0.002 TYR B1411 ARG 0.003 0.000 ARG A1153 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 640) hydrogen bonds : angle 5.22861 ( 1842) SS BOND : bond 0.00301 ( 14) SS BOND : angle 1.41212 ( 28) covalent geometry : bond 0.00589 (19527) covalent geometry : angle 0.62111 (26506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 178 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 267 ILE cc_start: 0.9136 (mm) cc_final: 0.8752 (mt) REVERT: C 276 LYS cc_start: 0.8471 (mmmt) cc_final: 0.7998 (mptt) REVERT: C 554 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8953 (mt) REVERT: A 796 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8776 (p) REVERT: A 804 ILE cc_start: 0.9086 (mm) cc_final: 0.8846 (mm) REVERT: A 826 GLU cc_start: 0.8330 (pm20) cc_final: 0.7550 (pm20) REVERT: A 917 TRP cc_start: 0.7591 (t-100) cc_final: 0.7215 (m100) REVERT: A 935 LYS cc_start: 0.8659 (ttpt) cc_final: 0.7801 (mttm) REVERT: A 988 LEU cc_start: 0.8878 (mm) cc_final: 0.8632 (mp) REVERT: A 1024 TYR cc_start: 0.7892 (t80) cc_final: 0.7664 (t80) REVERT: A 1161 LEU cc_start: 0.8566 (mm) cc_final: 0.7785 (tt) REVERT: A 1247 MET cc_start: 0.8177 (ttm) cc_final: 0.7862 (ttm) REVERT: A 1259 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7789 (tt) REVERT: B 107 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7496 (mt0) REVERT: B 183 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.6937 (p90) REVERT: B 264 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8500 (tt) REVERT: B 315 TYR cc_start: 0.8118 (p90) cc_final: 0.7744 (p90) REVERT: B 321 MET cc_start: 0.8376 (mtt) cc_final: 0.8107 (mtt) REVERT: B 453 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7735 (tm-30) REVERT: B 811 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7029 (tpt) REVERT: B 1467 LYS cc_start: 0.7929 (mmmm) cc_final: 0.7713 (mmmt) REVERT: B 1481 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7360 (pp) outliers start: 82 outliers final: 65 residues processed: 244 average time/residue: 0.2808 time to fit residues: 109.8801 Evaluate side-chains 248 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 175 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1014 SER Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1341 LEU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1489 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 811 MET Chi-restraints excluded: chain B residue 838 ASN Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 1378 THR Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1480 LEU Chi-restraints excluded: chain B residue 1481 LEU Chi-restraints excluded: chain B residue 1482 ASN Chi-restraints excluded: chain B residue 1485 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 107 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 178 optimal weight: 0.0670 chunk 110 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 1 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 211 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS ** B1473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.121820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099314 restraints weight = 34893.303| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.51 r_work: 0.3070 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19541 Z= 0.098 Angle : 0.523 9.285 26534 Z= 0.266 Chirality : 0.045 0.160 3024 Planarity : 0.003 0.052 3374 Dihedral : 4.895 52.216 2628 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.75 % Allowed : 19.17 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.17), residues: 2396 helix: -0.71 (0.28), residues: 328 sheet: -0.15 (0.17), residues: 936 loop : -1.48 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1106 HIS 0.004 0.001 HIS C 226 PHE 0.013 0.001 PHE B 347 TYR 0.023 0.001 TYR B1411 ARG 0.002 0.000 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.02819 ( 640) hydrogen bonds : angle 4.81776 ( 1842) SS BOND : bond 0.00224 ( 14) SS BOND : angle 1.12764 ( 28) covalent geometry : bond 0.00228 (19527) covalent geometry : angle 0.52187 (26506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 194 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 253 ARG cc_start: 0.7661 (ptp-110) cc_final: 0.7347 (ptt90) REVERT: C 267 ILE cc_start: 0.9051 (mm) cc_final: 0.8652 (mt) REVERT: C 276 LYS cc_start: 0.8442 (mmmt) cc_final: 0.7991 (mptt) REVERT: C 554 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8973 (mt) REVERT: A 804 ILE cc_start: 0.8922 (mm) cc_final: 0.8660 (mm) REVERT: A 826 GLU cc_start: 0.8156 (pm20) cc_final: 0.7495 (pm20) REVERT: A 917 TRP cc_start: 0.7536 (t-100) cc_final: 0.7268 (m100) REVERT: A 935 LYS cc_start: 0.8580 (ttpt) cc_final: 0.7702 (mttm) REVERT: A 988 LEU cc_start: 0.8834 (mm) cc_final: 0.8567 (mp) REVERT: A 1024 TYR cc_start: 0.7818 (t80) cc_final: 0.7614 (t80) REVERT: A 1044 LYS cc_start: 0.6996 (mmmt) cc_final: 0.6712 (tttm) REVERT: A 1144 LEU cc_start: 0.8379 (tp) cc_final: 0.8166 (mt) REVERT: A 1161 LEU cc_start: 0.8497 (mm) cc_final: 0.7681 (tt) REVERT: A 1247 MET cc_start: 0.8098 (ttm) cc_final: 0.7858 (ttm) REVERT: A 1259 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7773 (tt) REVERT: B 183 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.6729 (p90) REVERT: B 264 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8497 (tt) REVERT: B 315 TYR cc_start: 0.7996 (p90) cc_final: 0.7674 (p90) REVERT: B 321 MET cc_start: 0.8354 (mtt) cc_final: 0.8113 (mtt) REVERT: B 453 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7630 (tm-30) REVERT: B 1379 MET cc_start: 0.7953 (mmm) cc_final: 0.7631 (mmm) REVERT: B 1402 LYS cc_start: 0.7599 (mtmt) cc_final: 0.7273 (ptmt) REVERT: B 1467 LYS cc_start: 0.7867 (mmmm) cc_final: 0.7660 (mmmt) REVERT: B 1481 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7219 (pp) outliers start: 59 outliers final: 47 residues processed: 242 average time/residue: 0.3086 time to fit residues: 118.2773 Evaluate side-chains 235 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1341 LEU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 1378 THR Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1481 LEU Chi-restraints excluded: chain B residue 1485 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 198 optimal weight: 6.9990 chunk 188 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 194 optimal weight: 0.3980 chunk 169 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 656 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 GLN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.122323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.099632 restraints weight = 34956.320| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.41 r_work: 0.3077 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 19541 Z= 0.102 Angle : 0.522 9.715 26534 Z= 0.263 Chirality : 0.045 0.178 3024 Planarity : 0.003 0.050 3374 Dihedral : 4.719 49.026 2628 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.52 % Allowed : 19.73 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2396 helix: -0.48 (0.28), residues: 328 sheet: -0.02 (0.18), residues: 928 loop : -1.38 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1106 HIS 0.008 0.001 HIS B 312 PHE 0.011 0.001 PHE B 347 TYR 0.022 0.001 TYR B1411 ARG 0.002 0.000 ARG B1399 Details of bonding type rmsd hydrogen bonds : bond 0.02779 ( 640) hydrogen bonds : angle 4.69086 ( 1842) SS BOND : bond 0.00220 ( 14) SS BOND : angle 1.07558 ( 28) covalent geometry : bond 0.00244 (19527) covalent geometry : angle 0.52072 (26506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 190 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 175 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: C 253 ARG cc_start: 0.7700 (ptp-110) cc_final: 0.7398 (ptt90) REVERT: C 267 ILE cc_start: 0.9037 (mm) cc_final: 0.8638 (mt) REVERT: C 276 LYS cc_start: 0.8446 (mmmt) cc_final: 0.7984 (mptt) REVERT: C 554 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8946 (mt) REVERT: A 804 ILE cc_start: 0.8891 (mm) cc_final: 0.8599 (mm) REVERT: A 826 GLU cc_start: 0.8110 (pm20) cc_final: 0.7436 (pm20) REVERT: A 917 TRP cc_start: 0.7533 (t-100) cc_final: 0.7267 (m100) REVERT: A 988 LEU cc_start: 0.8833 (mm) cc_final: 0.8568 (mp) REVERT: A 1005 LYS cc_start: 0.8407 (mtpt) cc_final: 0.7962 (mmmm) REVERT: A 1024 TYR cc_start: 0.7815 (t80) cc_final: 0.7556 (t80) REVERT: A 1044 LYS cc_start: 0.7015 (mmmt) cc_final: 0.6741 (tttm) REVERT: A 1138 ARG cc_start: 0.8101 (mtm-85) cc_final: 0.7869 (ptp90) REVERT: A 1161 LEU cc_start: 0.8373 (mm) cc_final: 0.7569 (tt) REVERT: A 1214 ARG cc_start: 0.7850 (ttm170) cc_final: 0.7466 (mtm-85) REVERT: A 1259 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7790 (tt) REVERT: B 107 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7513 (mt0) REVERT: B 183 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.6730 (p90) REVERT: B 264 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8546 (tt) REVERT: B 315 TYR cc_start: 0.8039 (p90) cc_final: 0.7653 (p90) REVERT: B 321 MET cc_start: 0.8357 (mtt) cc_final: 0.8124 (mtt) REVERT: B 453 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7635 (tm-30) REVERT: B 811 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.6941 (tpt) REVERT: B 1379 MET cc_start: 0.7921 (mmm) cc_final: 0.7607 (mmm) REVERT: B 1467 LYS cc_start: 0.7869 (mmmm) cc_final: 0.7557 (mmmt) REVERT: B 1481 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7323 (pp) outliers start: 54 outliers final: 41 residues processed: 230 average time/residue: 0.3062 time to fit residues: 112.2562 Evaluate side-chains 231 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1341 LEU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 811 MET Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 1378 THR Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1481 LEU Chi-restraints excluded: chain B residue 1485 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 65 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 HIS ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 656 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 GLN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 ASN B1428 ASN ** B1473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.117154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.094714 restraints weight = 34897.337| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.47 r_work: 0.2979 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 19541 Z= 0.278 Angle : 0.654 14.652 26534 Z= 0.332 Chirality : 0.048 0.180 3024 Planarity : 0.004 0.049 3374 Dihedral : 5.494 49.784 2628 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.35 % Favored : 92.61 % Rotamer: Outliers : 2.80 % Allowed : 20.10 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.17), residues: 2396 helix: -0.70 (0.27), residues: 329 sheet: -0.24 (0.17), residues: 950 loop : -1.43 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1106 HIS 0.011 0.001 HIS B 312 PHE 0.021 0.002 PHE B 464 TYR 0.025 0.002 TYR B1411 ARG 0.004 0.000 ARG A1153 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 640) hydrogen bonds : angle 5.19605 ( 1842) SS BOND : bond 0.00314 ( 14) SS BOND : angle 1.27341 ( 28) covalent geometry : bond 0.00668 (19527) covalent geometry : angle 0.65336 (26506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 173 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 267 ILE cc_start: 0.9160 (mm) cc_final: 0.8784 (mt) REVERT: C 276 LYS cc_start: 0.8416 (mmmt) cc_final: 0.7969 (mptt) REVERT: C 554 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8964 (mt) REVERT: A 796 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8768 (p) REVERT: A 804 ILE cc_start: 0.9103 (mm) cc_final: 0.8853 (mm) REVERT: A 917 TRP cc_start: 0.7681 (t-100) cc_final: 0.7324 (m100) REVERT: A 935 LYS cc_start: 0.8645 (ttpt) cc_final: 0.7759 (mttm) REVERT: A 1024 TYR cc_start: 0.7888 (t80) cc_final: 0.7633 (t80) REVERT: A 1161 LEU cc_start: 0.8446 (mm) cc_final: 0.7633 (tt) REVERT: A 1259 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7794 (tt) REVERT: B 107 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7522 (mt0) REVERT: B 183 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.6932 (p90) REVERT: B 264 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8515 (tt) REVERT: B 321 MET cc_start: 0.8442 (mtt) cc_final: 0.8218 (mtt) REVERT: B 453 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7789 (tm-30) REVERT: B 811 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7121 (tpt) REVERT: B 1467 LYS cc_start: 0.7822 (mmmm) cc_final: 0.7553 (mmmt) REVERT: B 1481 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7405 (pp) outliers start: 60 outliers final: 44 residues processed: 219 average time/residue: 0.3187 time to fit residues: 110.5648 Evaluate side-chains 219 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 167 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1014 SER Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1341 LEU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 811 MET Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1481 LEU Chi-restraints excluded: chain B residue 1485 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 77 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 193 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 169 optimal weight: 7.9990 chunk 90 optimal weight: 0.0020 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1121 ASN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.121494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.098590 restraints weight = 35017.705| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.45 r_work: 0.3065 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19541 Z= 0.109 Angle : 0.543 10.214 26534 Z= 0.275 Chirality : 0.045 0.156 3024 Planarity : 0.004 0.051 3374 Dihedral : 4.939 49.419 2628 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.38 % Allowed : 20.71 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2396 helix: -0.40 (0.28), residues: 328 sheet: -0.11 (0.17), residues: 933 loop : -1.33 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1106 HIS 0.009 0.001 HIS B 46 PHE 0.013 0.001 PHE B 347 TYR 0.022 0.001 TYR B1411 ARG 0.002 0.000 ARG A1138 Details of bonding type rmsd hydrogen bonds : bond 0.02908 ( 640) hydrogen bonds : angle 4.83311 ( 1842) SS BOND : bond 0.00226 ( 14) SS BOND : angle 1.08335 ( 28) covalent geometry : bond 0.00256 (19527) covalent geometry : angle 0.54171 (26506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8146.85 seconds wall clock time: 142 minutes 49.38 seconds (8569.38 seconds total)