Starting phenix.real_space_refine on Sat Sep 28 12:47:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ayh_15713/09_2024/8ayh_15713.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ayh_15713/09_2024/8ayh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ayh_15713/09_2024/8ayh_15713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ayh_15713/09_2024/8ayh_15713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ayh_15713/09_2024/8ayh_15713.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ayh_15713/09_2024/8ayh_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-5461/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: 11.00, per 1000 atoms: 0.58 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: 4.56 Conformation dependent library (CDL) restraints added in 2.6 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: 2.88 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: 9.59 Time building geometry restraints manager: 5.28 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: 1.880 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: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 45.680 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.000 ------------------------------------------------------------------------------- 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 19527 Z= 0.490 Angle : 0.912 12.373 26506 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 *********************** 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 fitting. rotamer outliers: 14 poor density : 286 time to evaluate : 2.256 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: 0.3259 time to fit residues: 146.2637 Evaluate side-chains 185 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 176 time to evaluate : 2.263 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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 19527 Z= 0.219 Angle : 0.593 10.334 26506 Z= 0.310 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 *********************** 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 fitting. rotamer outliers: 43 poor density : 223 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 193 ASN cc_start: 0.8227 (t0) cc_final: 0.8013 (t0) REVERT: C 276 LYS cc_start: 0.8355 (mmmt) cc_final: 0.7908 (mptt) REVERT: C 339 GLU cc_start: 0.7620 (mp0) cc_final: 0.7397 (mp0) REVERT: A 804 ILE cc_start: 0.9043 (mm) cc_final: 0.8791 (mm) REVERT: A 1024 TYR cc_start: 0.7477 (t80) cc_final: 0.7259 (t80) REVERT: B 453 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7332 (tm-30) outliers start: 43 outliers final: 30 residues processed: 257 average time/residue: 0.2947 time to fit residues: 120.5215 Evaluate side-chains 216 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 186 time to evaluate : 2.051 ------------------------------------------------------------------------------- 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 121 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 216 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 C 656 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 GLN A1178 ASN A1360 HIS B 65 GLN B 305 ASN B 485 ASN ** B 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1346 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 19527 Z= 0.425 Angle : 0.654 13.326 26506 Z= 0.336 Chirality : 0.048 0.183 3024 Planarity : 0.005 0.050 3374 Dihedral : 5.885 50.526 2628 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.89 % Favored : 93.07 % Rotamer: Outliers : 3.50 % Allowed : 16.09 % Favored : 80.41 % 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: -2.59 (0.16), residues: 2396 helix: -2.25 (0.24), residues: 326 sheet: -1.10 (0.16), residues: 956 loop : -2.03 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1106 HIS 0.008 0.001 HIS C 226 PHE 0.018 0.002 PHE B 464 TYR 0.022 0.002 TYR C 457 ARG 0.003 0.000 ARG A 766 *********************** 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 261 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 186 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 339 GLU cc_start: 0.7698 (mp0) cc_final: 0.7482 (mp0) REVERT: C 554 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8963 (mt) REVERT: A 786 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8405 (pp) REVERT: A 796 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8686 (p) REVERT: A 804 ILE cc_start: 0.9042 (mm) cc_final: 0.8794 (mm) REVERT: A 917 TRP cc_start: 0.6918 (t-100) cc_final: 0.6586 (m100) REVERT: A 988 LEU cc_start: 0.8928 (mm) cc_final: 0.8695 (mp) REVERT: A 1024 TYR cc_start: 0.7605 (t80) cc_final: 0.7375 (t80) REVERT: A 1057 MET cc_start: 0.7872 (tpp) cc_final: 0.7531 (ttm) REVERT: B 107 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7352 (mt0) REVERT: B 264 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8492 (tt) REVERT: B 453 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7333 (tm-30) outliers start: 75 outliers final: 54 residues processed: 248 average time/residue: 0.2717 time to fit residues: 108.4057 Evaluate side-chains 230 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 171 time to evaluate : 2.146 ------------------------------------------------------------------------------- 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 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 359 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 446 ASN 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 786 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 930 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 1278 GLN Chi-restraints excluded: chain A residue 1347 ILE 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 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 427 THR Chi-restraints excluded: chain B residue 431 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 838 ASN Chi-restraints excluded: chain B residue 851 LEU 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 215 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 146 optimal weight: 0.0170 chunk 219 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 446 ASN C 644 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 GLN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN B 485 ASN ** B 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19527 Z= 0.166 Angle : 0.536 9.761 26506 Z= 0.278 Chirality : 0.045 0.162 3024 Planarity : 0.004 0.050 3374 Dihedral : 5.262 53.055 2628 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.85 % Allowed : 17.49 % 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: -2.10 (0.16), residues: 2396 helix: -1.59 (0.27), residues: 327 sheet: -0.72 (0.16), residues: 936 loop : -1.87 (0.17), residues: 1133 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 0.012 0.001 TYR A1317 ARG 0.002 0.000 ARG B 227 *********************** 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 275 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 214 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 175 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: A 796 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8587 (p) REVERT: A 804 ILE cc_start: 0.8886 (mm) cc_final: 0.8634 (mm) REVERT: A 1161 LEU cc_start: 0.8635 (mm) cc_final: 0.7970 (tt) REVERT: B 350 THR cc_start: 0.8726 (t) cc_final: 0.8524 (t) REVERT: B 1481 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7167 (pp) outliers start: 61 outliers final: 43 residues processed: 257 average time/residue: 0.2840 time to fit residues: 116.5116 Evaluate side-chains 231 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 185 time to evaluate : 2.184 ------------------------------------------------------------------------------- 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 446 ASN 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 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 833 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 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 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 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 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 1347 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 160 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 208 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** 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 446 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 GLN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 ASN B 838 ASN B1452 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 19527 Z= 0.353 Angle : 0.610 11.964 26506 Z= 0.311 Chirality : 0.047 0.172 3024 Planarity : 0.004 0.047 3374 Dihedral : 5.527 58.783 2628 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.43 % Favored : 93.53 % Rotamer: Outliers : 3.59 % Allowed : 18.19 % Favored : 78.22 % 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: -1.92 (0.17), residues: 2396 helix: -1.31 (0.27), residues: 330 sheet: -0.63 (0.17), residues: 933 loop : -1.76 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1106 HIS 0.006 0.001 HIS C 226 PHE 0.016 0.002 PHE B 464 TYR 0.024 0.001 TYR B1411 ARG 0.004 0.000 ARG C 449 *********************** 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 257 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 180 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 276 LYS cc_start: 0.8411 (mmmt) cc_final: 0.7939 (mptt) REVERT: C 444 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7396 (tm-30) REVERT: C 554 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8944 (mt) REVERT: A 796 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8698 (p) REVERT: A 804 ILE cc_start: 0.8953 (mm) cc_final: 0.8703 (mm) REVERT: A 826 GLU cc_start: 0.8088 (pm20) cc_final: 0.7353 (pm20) REVERT: A 988 LEU cc_start: 0.8917 (mm) cc_final: 0.8669 (mp) REVERT: A 1206 ARG cc_start: 0.7701 (tpp80) cc_final: 0.7242 (mpp-170) REVERT: A 1259 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7891 (tt) REVERT: B 107 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7339 (mt0) REVERT: B 183 PHE cc_start: 0.7613 (OUTLIER) cc_final: 0.6873 (p90) REVERT: B 264 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8464 (tt) REVERT: B 1481 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7236 (pp) outliers start: 77 outliers final: 56 residues processed: 245 average time/residue: 0.2993 time to fit residues: 118.6645 Evaluate side-chains 234 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 171 time to evaluate : 2.166 ------------------------------------------------------------------------------- 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 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 359 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 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 833 VAL 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 1259 LEU Chi-restraints excluded: chain A residue 1341 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 136 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 19527 Z= 0.330 Angle : 0.594 11.466 26506 Z= 0.303 Chirality : 0.047 0.164 3024 Planarity : 0.004 0.048 3374 Dihedral : 5.495 58.535 2628 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 4.29 % Allowed : 18.10 % Favored : 77.61 % 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: -1.73 (0.17), residues: 2396 helix: -1.11 (0.27), residues: 328 sheet: -0.50 (0.17), residues: 938 loop : -1.68 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1106 HIS 0.006 0.001 HIS C 226 PHE 0.015 0.002 PHE C 217 TYR 0.024 0.001 TYR B1411 ARG 0.003 0.000 ARG C 449 *********************** 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 271 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 179 time to evaluate : 2.067 Fit side-chains revert: symmetry clash REVERT: C 276 LYS cc_start: 0.8409 (mmmt) cc_final: 0.7952 (mptt) REVERT: C 444 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7518 (tm-30) REVERT: C 554 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8948 (mt) REVERT: A 796 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8721 (p) REVERT: A 804 ILE cc_start: 0.8969 (mm) cc_final: 0.8750 (mm) REVERT: A 826 GLU cc_start: 0.8076 (pm20) cc_final: 0.7404 (pm20) REVERT: A 935 LYS cc_start: 0.8488 (ttpt) cc_final: 0.7747 (mttm) REVERT: A 988 LEU cc_start: 0.8933 (mm) cc_final: 0.8704 (mp) REVERT: A 1161 LEU cc_start: 0.8579 (mm) cc_final: 0.7897 (tt) REVERT: A 1259 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7858 (tt) REVERT: B 107 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7327 (mt0) REVERT: B 183 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.6944 (p90) REVERT: B 264 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8449 (tt) REVERT: B 411 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.9083 (pt) REVERT: B 811 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.6538 (tpt) REVERT: B 1467 LYS cc_start: 0.7970 (mmmm) cc_final: 0.7735 (mmmt) REVERT: B 1481 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7248 (pp) outliers start: 92 outliers final: 65 residues processed: 256 average time/residue: 0.2725 time to fit residues: 112.5412 Evaluate side-chains 248 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 174 time to evaluate : 2.248 ------------------------------------------------------------------------------- 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 359 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 833 VAL 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 1361 VAL 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 260 VAL 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 411 ILE 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 1402 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 231 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 644 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 19527 Z= 0.247 Angle : 0.560 11.292 26506 Z= 0.285 Chirality : 0.046 0.164 3024 Planarity : 0.004 0.049 3374 Dihedral : 5.253 55.115 2628 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.80 % Favored : 94.16 % Rotamer: Outliers : 3.82 % Allowed : 19.12 % Favored : 77.05 % 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: -1.57 (0.17), residues: 2396 helix: -1.00 (0.28), residues: 328 sheet: -0.37 (0.17), residues: 943 loop : -1.60 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1106 HIS 0.005 0.001 HIS A1202 PHE 0.014 0.001 PHE B 347 TYR 0.020 0.001 TYR B1411 ARG 0.002 0.000 ARG B 227 *********************** 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 257 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 175 time to evaluate : 2.197 Fit side-chains revert: symmetry clash REVERT: C 276 LYS cc_start: 0.8437 (mmmt) cc_final: 0.8000 (mptt) REVERT: C 444 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7418 (tm-30) REVERT: C 554 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8935 (mt) REVERT: A 796 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8686 (p) REVERT: A 804 ILE cc_start: 0.8890 (mm) cc_final: 0.8662 (mm) REVERT: A 826 GLU cc_start: 0.8002 (pm20) cc_final: 0.7427 (pm20) REVERT: A 935 LYS cc_start: 0.8464 (ttpt) cc_final: 0.7746 (mttm) REVERT: A 988 LEU cc_start: 0.8927 (mm) cc_final: 0.8695 (mp) REVERT: A 1161 LEU cc_start: 0.8568 (mm) cc_final: 0.7851 (tt) REVERT: B 107 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7188 (mt0) REVERT: B 183 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.6904 (p90) REVERT: B 264 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8436 (tp) REVERT: B 411 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.9051 (pt) REVERT: B 811 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.6546 (tpt) REVERT: B 1467 LYS cc_start: 0.7974 (mmmm) cc_final: 0.7685 (mmmt) REVERT: B 1481 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7213 (pp) outliers start: 82 outliers final: 63 residues processed: 240 average time/residue: 0.2706 time to fit residues: 105.3298 Evaluate side-chains 241 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 170 time to evaluate : 2.097 ------------------------------------------------------------------------------- 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 644 ASN 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 833 VAL 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 1341 LEU Chi-restraints excluded: chain A residue 1347 ILE 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 260 VAL 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 411 ILE 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 577 LEU Chi-restraints excluded: chain B residue 636 THR 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 1402 LYS Chi-restraints excluded: chain B residue 1481 LEU 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 143 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 chunk 44 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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** C 644 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19527 Z= 0.212 Angle : 0.544 10.780 26506 Z= 0.277 Chirality : 0.045 0.182 3024 Planarity : 0.004 0.050 3374 Dihedral : 5.104 52.692 2628 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.50 % Allowed : 19.45 % Favored : 77.05 % 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: -1.42 (0.17), residues: 2396 helix: -0.86 (0.28), residues: 328 sheet: -0.26 (0.17), residues: 941 loop : -1.52 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1106 HIS 0.005 0.001 HIS A1202 PHE 0.014 0.001 PHE B 347 TYR 0.020 0.001 TYR B1411 ARG 0.002 0.000 ARG B 227 *********************** 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 256 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 181 time to evaluate : 2.911 Fit side-chains revert: symmetry clash REVERT: C 267 ILE cc_start: 0.8974 (mm) cc_final: 0.8606 (mt) REVERT: C 276 LYS cc_start: 0.8441 (mmmt) cc_final: 0.8011 (mptt) REVERT: C 444 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7464 (tm-30) REVERT: C 554 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8933 (mt) REVERT: A 796 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8677 (p) REVERT: A 804 ILE cc_start: 0.8833 (mm) cc_final: 0.8589 (mm) REVERT: A 826 GLU cc_start: 0.7961 (pm20) cc_final: 0.7590 (pt0) REVERT: A 935 LYS cc_start: 0.8448 (ttpt) cc_final: 0.7751 (mttm) REVERT: A 988 LEU cc_start: 0.8912 (mm) cc_final: 0.8675 (mp) REVERT: A 1161 LEU cc_start: 0.8533 (mm) cc_final: 0.7789 (tt) REVERT: A 1259 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7865 (tt) REVERT: B 107 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.7184 (mt0) REVERT: B 183 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.6904 (p90) REVERT: B 264 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8441 (tt) REVERT: B 350 THR cc_start: 0.8763 (t) cc_final: 0.8560 (t) REVERT: B 411 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.9035 (pt) REVERT: B 811 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.6534 (tpt) REVERT: B 1467 LYS cc_start: 0.7967 (mmmm) cc_final: 0.7687 (mmmt) REVERT: B 1481 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7278 (pp) outliers start: 75 outliers final: 60 residues processed: 241 average time/residue: 0.2669 time to fit residues: 103.8150 Evaluate side-chains 241 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 172 time to evaluate : 1.966 ------------------------------------------------------------------------------- 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 359 THR 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 777 VAL 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 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 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 1259 LEU Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1341 LEU Chi-restraints excluded: chain A residue 1347 ILE 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 364 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 411 ILE 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 636 THR 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 1402 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 202 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** C 644 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 19527 Z= 0.344 Angle : 0.602 12.619 26506 Z= 0.305 Chirality : 0.047 0.166 3024 Planarity : 0.004 0.048 3374 Dihedral : 5.366 51.035 2628 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.76 % Favored : 93.20 % Rotamer: Outliers : 3.50 % Allowed : 19.96 % Favored : 76.54 % 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: -1.45 (0.17), residues: 2396 helix: -0.86 (0.28), residues: 329 sheet: -0.32 (0.17), residues: 945 loop : -1.51 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1106 HIS 0.006 0.001 HIS C 226 PHE 0.015 0.002 PHE C 217 TYR 0.019 0.001 TYR B1411 ARG 0.003 0.000 ARG A1153 *********************** 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 249 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 174 time to evaluate : 2.351 Fit side-chains revert: symmetry clash REVERT: C 267 ILE cc_start: 0.9035 (mm) cc_final: 0.8671 (mt) REVERT: C 276 LYS cc_start: 0.8470 (mmmt) cc_final: 0.8052 (mptt) REVERT: C 554 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8945 (mt) REVERT: A 796 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8722 (p) REVERT: A 804 ILE cc_start: 0.8937 (mm) cc_final: 0.8708 (mm) REVERT: A 826 GLU cc_start: 0.8009 (pm20) cc_final: 0.7764 (pt0) REVERT: A 935 LYS cc_start: 0.8480 (ttpt) cc_final: 0.7752 (mttm) REVERT: A 988 LEU cc_start: 0.8939 (mm) cc_final: 0.8693 (mp) REVERT: A 1161 LEU cc_start: 0.8484 (mm) cc_final: 0.7738 (tt) REVERT: A 1259 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7842 (tt) REVERT: B 107 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.7147 (mt0) REVERT: B 183 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7018 (p90) REVERT: B 264 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8445 (tt) REVERT: B 411 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9080 (pt) REVERT: B 811 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.6570 (tpt) REVERT: B 1467 LYS cc_start: 0.7953 (mmmm) cc_final: 0.7671 (mmmt) REVERT: B 1481 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7384 (pp) outliers start: 75 outliers final: 63 residues processed: 233 average time/residue: 0.2821 time to fit residues: 106.0341 Evaluate side-chains 241 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 169 time to evaluate : 2.247 ------------------------------------------------------------------------------- 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 359 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 777 VAL 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 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 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 1259 LEU Chi-restraints excluded: chain A residue 1341 LEU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1489 SER Chi-restraints excluded: chain B residue 26 THR 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 260 VAL 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 364 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 411 ILE 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 636 THR 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 1402 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 4.9990 chunk 227 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 239 optimal weight: 7.9990 chunk 220 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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** C 644 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS B1419 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19527 Z= 0.190 Angle : 0.541 10.157 26506 Z= 0.274 Chirality : 0.045 0.165 3024 Planarity : 0.004 0.052 3374 Dihedral : 4.998 50.041 2628 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.22 % Allowed : 20.34 % Favored : 76.45 % 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: -1.25 (0.17), residues: 2396 helix: -0.65 (0.28), residues: 328 sheet: -0.16 (0.17), residues: 924 loop : -1.41 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1106 HIS 0.004 0.001 HIS C 226 PHE 0.015 0.001 PHE B 347 TYR 0.016 0.001 TYR B1411 ARG 0.002 0.000 ARG B1399 ********************** 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 256 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 187 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 267 ILE cc_start: 0.8967 (mm) cc_final: 0.8595 (mt) REVERT: C 276 LYS cc_start: 0.8436 (mmmt) cc_final: 0.8038 (mptt) REVERT: C 554 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8948 (mt) REVERT: A 796 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8651 (p) REVERT: A 804 ILE cc_start: 0.8794 (mm) cc_final: 0.8559 (mm) REVERT: A 826 GLU cc_start: 0.7830 (pm20) cc_final: 0.7622 (pt0) REVERT: A 988 LEU cc_start: 0.8922 (mm) cc_final: 0.8662 (mp) REVERT: A 1005 LYS cc_start: 0.8110 (mtpt) cc_final: 0.7904 (mtpp) REVERT: A 1092 TYR cc_start: 0.7618 (m-80) cc_final: 0.7353 (m-80) REVERT: A 1161 LEU cc_start: 0.8392 (mm) cc_final: 0.7643 (tt) REVERT: A 1214 ARG cc_start: 0.7687 (ttm170) cc_final: 0.7244 (mtm-85) REVERT: A 1259 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7790 (tt) REVERT: B 107 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.7116 (mt0) REVERT: B 183 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.6999 (p90) REVERT: B 264 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8484 (tt) REVERT: B 811 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.6541 (tpt) REVERT: B 1467 LYS cc_start: 0.7897 (mmmm) cc_final: 0.7591 (mmmt) REVERT: B 1481 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7339 (pp) outliers start: 69 outliers final: 58 residues processed: 242 average time/residue: 0.2780 time to fit residues: 107.2375 Evaluate side-chains 241 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 175 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 47 THR 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 359 THR 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 644 ASN Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 777 VAL 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 833 VAL Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 942 VAL 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 1259 LEU Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1341 LEU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1489 SER 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 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 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 636 THR 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 1402 LYS 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 151 optimal weight: 0.9980 chunk 202 optimal weight: 0.0570 chunk 58 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 190 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 195 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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** C 644 ASN C 656 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** 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 = 0.3589 r_free = 0.3589 target = 0.122058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.099468 restraints weight = 34994.539| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.51 r_work: 0.3077 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19527 Z= 0.160 Angle : 0.531 9.337 26506 Z= 0.268 Chirality : 0.045 0.174 3024 Planarity : 0.004 0.051 3374 Dihedral : 4.807 47.502 2628 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.80 % Allowed : 21.22 % Favored : 75.98 % 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: -0.49 (0.28), residues: 327 sheet: -0.02 (0.17), residues: 921 loop : -1.36 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1106 HIS 0.005 0.001 HIS A1202 PHE 0.013 0.001 PHE B 347 TYR 0.016 0.001 TYR B1411 ARG 0.002 0.000 ARG A1138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3785.52 seconds wall clock time: 68 minutes 51.01 seconds (4131.01 seconds total)