Starting phenix.real_space_refine on Sat Jul 4 07:24:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ayh_15713/07_2026/8ayh_15713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ayh_15713/07_2026/8ayh_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8ayh_15713/07_2026/8ayh_15713.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ayh_15713/07_2026/8ayh_15713.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ayh_15713/07_2026/8ayh_15713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ayh_15713/07_2026/8ayh_15713.map" model { file = "/net/cci-nas-00/data/ceres_data/8ayh_15713/07_2026/8ayh_15713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ayh_15713/07_2026/8ayh_15713.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 3.90, per 1000 atoms: 0.20 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: 3.02 Conformation dependent library (CDL) restraints added in 718.5 milliseconds 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: 0.89 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: 4.68 Time building geometry restraints manager: 2.07 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: 10494 17.71 - 35.41: 1059 35.41 - 53.12: 182 53.12 - 70.82: 26 70.82 - 88.53: 13 Dihedral angle restraints: 11774 sinusoidal: 4706 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 11771 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: 1.860 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: 0.410 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.710 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 19541 Z= 0.317 Angle : 0.913 12.373 26534 Z= 0.499 Chirality : 0.056 0.257 3024 Planarity : 0.007 0.072 3374 Dihedral : 14.436 88.529 7182 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.97 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG A 717 TYR 0.030 0.002 TYR C 240 PHE 0.024 0.003 PHE C 217 TRP 0.016 0.002 TRP A 917 HIS 0.006 0.001 HIS A1421 Details of bonding type rmsd/Z covalent geometry : bond 0.00739 / 0.32 (19527) covalent geometry : angle 0.91181 / 0.50 (26506) SS BOND : bond 0.00290 / 0.16 ( 14) SS BOND : angle 1.53240 / 0.99 ( 28) hydrogen bonds : bond 0.26682 / 17.20 ( 640) hydrogen bonds : angle 9.76940 / 6.62 ( 1842) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 286 time to evaluate : 0.828 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: 0.1519 time to fit residues: 69.0666 Evaluate side-chains 185 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.5980 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 80 GLN C 399 GLN 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 B1419 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.098619 restraints weight = 34917.443| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.48 r_work: 0.3042 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19541 Z= 0.127 Angle : 0.587 9.899 26534 Z= 0.307 Chirality : 0.046 0.198 3024 Planarity : 0.005 0.053 3374 Dihedral : 5.671 46.636 2618 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.01 % Allowed : 13.95 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.15), residues: 2396 helix: -2.97 (0.22), residues: 320 sheet: -1.34 (0.16), residues: 929 loop : -2.21 (0.16), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 766 TYR 0.014 0.001 TYR A1092 PHE 0.026 0.001 PHE A 820 TRP 0.013 0.001 TRP A1106 HIS 0.004 0.001 HIS B1445 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (19527) covalent geometry : angle 0.58601 / 0.31 (26506) SS BOND : bond 0.01230 / 0.89 ( 14) SS BOND : angle 1.21459 / 0.73 ( 28) hydrogen bonds : bond 0.04095 / 2.61 ( 640) hydrogen bonds : angle 6.15453 / 4.16 ( 1842) *********************** 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 275 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 193 ASN cc_start: 0.8258 (t0) cc_final: 0.8034 (t0) REVERT: C 276 LYS cc_start: 0.8377 (mmmt) cc_final: 0.7899 (mptt) REVERT: C 339 GLU cc_start: 0.8098 (mp0) cc_final: 0.7831 (mp0) REVERT: A 804 ILE cc_start: 0.9155 (mm) cc_final: 0.8908 (mm) REVERT: A 935 LYS cc_start: 0.8600 (ttpt) cc_final: 0.7821 (mttm) REVERT: A 1024 TYR cc_start: 0.7682 (t80) cc_final: 0.7398 (t80) REVERT: A 1247 MET cc_start: 0.8261 (ttm) cc_final: 0.8046 (ttm) REVERT: B 453 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7853 (tm-30) outliers start: 43 outliers final: 30 residues processed: 265 average time/residue: 0.1348 time to fit residues: 56.8885 Evaluate side-chains 216 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 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 1378 THR 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 82 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 ASN C 533 ASN C 656 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 GLN A1360 HIS B 305 ASN ** B 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1346 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.119436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.096561 restraints weight = 35404.530| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.60 r_work: 0.3020 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 19541 Z= 0.188 Angle : 0.594 11.749 26534 Z= 0.306 Chirality : 0.047 0.179 3024 Planarity : 0.004 0.049 3374 Dihedral : 5.505 47.516 2616 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 3.12 % Allowed : 15.35 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.16), residues: 2396 helix: -2.28 (0.24), residues: 324 sheet: -1.01 (0.16), residues: 948 loop : -2.00 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 766 TYR 0.017 0.001 TYR C 457 PHE 0.015 0.002 PHE A 820 TRP 0.012 0.001 TRP A1106 HIS 0.006 0.001 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (19527) covalent geometry : angle 0.59356 / 0.31 (26506) SS BOND : bond 0.00295 / 0.20 ( 14) SS BOND : angle 1.14298 / 0.68 ( 28) hydrogen bonds : bond 0.03700 / 2.36 ( 640) hydrogen bonds : angle 5.59365 / 3.78 ( 1842) *********************** 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 262 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 195 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 339 GLU cc_start: 0.8125 (mp0) cc_final: 0.7875 (mp0) REVERT: C 554 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8967 (mt) REVERT: A 796 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8627 (p) REVERT: A 804 ILE cc_start: 0.9105 (mm) cc_final: 0.8823 (mm) REVERT: A 826 GLU cc_start: 0.8451 (pm20) cc_final: 0.7783 (pm20) REVERT: A 917 TRP cc_start: 0.7571 (t-100) cc_final: 0.7107 (m100) REVERT: A 1024 TYR cc_start: 0.7724 (t80) cc_final: 0.7484 (t80) REVERT: A 1057 MET cc_start: 0.7802 (tpp) cc_final: 0.7508 (ttm) REVERT: B 107 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7626 (mt0) REVERT: B 264 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8469 (tp) REVERT: B 453 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7810 (tm-30) outliers start: 67 outliers final: 49 residues processed: 246 average time/residue: 0.1354 time to fit residues: 53.3614 Evaluate side-chains 236 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 183 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 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 554 LEU Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 136 ILE 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 350 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 81 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 159 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 ASN C 644 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1178 ASN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 ASN B1452 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095657 restraints weight = 35279.043| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.57 r_work: 0.2992 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 19541 Z= 0.218 Angle : 0.603 12.159 26534 Z= 0.310 Chirality : 0.047 0.170 3024 Planarity : 0.004 0.048 3374 Dihedral : 5.538 52.738 2616 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.01 % Favored : 93.95 % Rotamer: Outliers : 3.73 % Allowed : 16.42 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.16), residues: 2396 helix: -1.75 (0.26), residues: 327 sheet: -0.79 (0.16), residues: 957 loop : -1.91 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 766 TYR 0.018 0.001 TYR C 457 PHE 0.015 0.002 PHE B 464 TRP 0.013 0.001 TRP A1106 HIS 0.006 0.001 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (19527) covalent geometry : angle 0.60206 / 0.31 (26506) SS BOND : bond 0.00285 / 0.19 ( 14) SS BOND : angle 1.32271 / 0.79 ( 28) hydrogen bonds : bond 0.03549 / 2.27 ( 640) hydrogen bonds : angle 5.42590 / 3.66 ( 1842) *********************** 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 269 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 189 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 253 ARG cc_start: 0.7613 (ptp-110) cc_final: 0.7361 (ptt90) REVERT: C 339 GLU cc_start: 0.8170 (mp0) cc_final: 0.7916 (mp0) REVERT: C 554 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8999 (mt) REVERT: A 796 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8661 (p) REVERT: A 804 ILE cc_start: 0.9119 (mm) cc_final: 0.8857 (mm) REVERT: A 826 GLU cc_start: 0.8428 (pm20) cc_final: 0.7691 (pm20) REVERT: A 917 TRP cc_start: 0.7614 (t-100) cc_final: 0.7294 (m100) REVERT: A 988 LEU cc_start: 0.8849 (mm) cc_final: 0.8607 (mp) REVERT: A 1024 TYR cc_start: 0.7774 (t80) cc_final: 0.7543 (t80) REVERT: A 1057 MET cc_start: 0.7817 (tpp) cc_final: 0.7602 (ttm) REVERT: A 1158 ILE cc_start: 0.8631 (mt) cc_final: 0.8367 (mt) REVERT: B 107 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7640 (mt0) REVERT: B 264 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8460 (tt) REVERT: B 453 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7814 (tm-30) REVERT: B 1481 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7296 (pp) outliers start: 80 outliers final: 61 residues processed: 252 average time/residue: 0.1331 time to fit residues: 53.9456 Evaluate side-chains 244 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 178 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 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 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 930 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 1144 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 105 VAL Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 350 THR 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 838 ASN Chi-restraints excluded: chain B residue 851 LEU 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 118 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 239 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 ASN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 GLN A1090 ASN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 ASN B1428 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.094252 restraints weight = 35261.806| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.50 r_work: 0.2986 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 19541 Z= 0.274 Angle : 0.642 12.983 26534 Z= 0.329 Chirality : 0.048 0.187 3024 Planarity : 0.004 0.046 3374 Dihedral : 5.721 58.706 2616 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.26 % Favored : 92.70 % Rotamer: Outliers : 4.20 % Allowed : 17.58 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.17), residues: 2396 helix: -1.51 (0.26), residues: 330 sheet: -0.75 (0.17), residues: 952 loop : -1.85 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 849 TYR 0.022 0.002 TYR C 457 PHE 0.018 0.002 PHE B 464 TRP 0.011 0.001 TRP A1106 HIS 0.007 0.001 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.27 (19527) covalent geometry : angle 0.64110 / 0.33 (26506) SS BOND : bond 0.00312 / 0.21 ( 14) SS BOND : angle 1.24017 / 0.76 ( 28) hydrogen bonds : bond 0.03645 / 2.33 ( 640) hydrogen bonds : angle 5.43335 / 3.65 ( 1842) *********************** 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 267 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 177 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 253 ARG cc_start: 0.7630 (ptp-110) cc_final: 0.7379 (ptt90) REVERT: C 554 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8989 (mt) REVERT: A 796 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8783 (p) REVERT: A 804 ILE cc_start: 0.9132 (mm) cc_final: 0.8898 (mm) REVERT: A 826 GLU cc_start: 0.8408 (pm20) cc_final: 0.7539 (pm20) REVERT: A 917 TRP cc_start: 0.7606 (t-100) cc_final: 0.7251 (m100) REVERT: A 988 LEU cc_start: 0.8870 (mm) cc_final: 0.8598 (mp) REVERT: A 1024 TYR cc_start: 0.7828 (t80) cc_final: 0.7557 (t80) REVERT: A 1158 ILE cc_start: 0.8659 (mt) cc_final: 0.8357 (mt) REVERT: A 1206 ARG cc_start: 0.7732 (tpp80) cc_final: 0.7495 (tpp-160) REVERT: A 1247 MET cc_start: 0.8176 (ttm) cc_final: 0.7870 (ttm) REVERT: A 1259 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7875 (tt) REVERT: B 107 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7636 (mt0) REVERT: B 183 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.6855 (p90) REVERT: B 264 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8476 (tt) REVERT: B 453 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7696 (tm-30) REVERT: B 764 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7120 (tm-30) REVERT: B 811 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.7080 (tpt) REVERT: B 1481 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7388 (pp) outliers start: 90 outliers final: 68 residues processed: 252 average time/residue: 0.1285 time to fit residues: 52.5267 Evaluate side-chains 249 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 172 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 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 930 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 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 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 350 THR Chi-restraints excluded: chain B residue 379 VAL 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 577 LEU Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 811 MET 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 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 117 optimal weight: 5.9990 chunk 219 optimal weight: 0.4980 chunk 104 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 220 optimal weight: 5.9990 chunk 20 optimal weight: 0.0060 chunk 155 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 312 HIS B 838 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.121774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099424 restraints weight = 34757.076| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.46 r_work: 0.3072 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19541 Z= 0.101 Angle : 0.520 8.553 26534 Z= 0.269 Chirality : 0.045 0.173 3024 Planarity : 0.004 0.051 3374 Dihedral : 5.016 59.355 2616 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.99 % Allowed : 19.03 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.17), residues: 2396 helix: -1.09 (0.28), residues: 328 sheet: -0.32 (0.17), residues: 909 loop : -1.71 (0.17), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 227 TYR 0.011 0.001 TYR B1411 PHE 0.014 0.001 PHE B 224 TRP 0.011 0.001 TRP C 469 HIS 0.005 0.001 HIS A1202 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (19527) covalent geometry : angle 0.51956 / 0.27 (26506) SS BOND : bond 0.00228 / 0.15 ( 14) SS BOND : angle 1.00635 / 0.56 ( 28) hydrogen bonds : bond 0.02860 / 1.84 ( 640) hydrogen bonds : angle 4.90460 / 3.31 ( 1842) *********************** 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 281 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 217 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: C 175 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: C 253 ARG cc_start: 0.7604 (ptp-110) cc_final: 0.7380 (ptt90) REVERT: C 276 LYS cc_start: 0.8365 (mmmt) cc_final: 0.7859 (mptt) REVERT: A 796 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8657 (p) REVERT: A 804 ILE cc_start: 0.8933 (mm) cc_final: 0.8673 (mm) REVERT: A 826 GLU cc_start: 0.8170 (pm20) cc_final: 0.7523 (pm20) REVERT: A 917 TRP cc_start: 0.7503 (t-100) cc_final: 0.7251 (m100) REVERT: A 935 LYS cc_start: 0.8581 (ttpt) cc_final: 0.7674 (mttm) REVERT: A 988 LEU cc_start: 0.8830 (mm) cc_final: 0.8550 (mp) REVERT: A 1005 LYS cc_start: 0.8372 (mtpt) cc_final: 0.7932 (mmmt) REVERT: A 1024 TYR cc_start: 0.7773 (t80) cc_final: 0.7519 (t80) REVERT: A 1161 LEU cc_start: 0.8624 (mm) cc_final: 0.7882 (tt) REVERT: A 1247 MET cc_start: 0.8206 (ttm) cc_final: 0.7979 (ttm) REVERT: B 183 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.6769 (p90) REVERT: B 453 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7571 (tm-30) REVERT: B 1467 LYS cc_start: 0.7910 (mmmm) cc_final: 0.7659 (mmmt) outliers start: 64 outliers final: 39 residues processed: 270 average time/residue: 0.1320 time to fit residues: 57.3950 Evaluate side-chains 230 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 333 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 654 LEU Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1341 LEU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1433 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 313 THR 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 379 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 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 1485 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 180 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 148 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 140 optimal weight: 0.7980 chunk 171 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 GLN A1178 ASN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096132 restraints weight = 35000.868| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.45 r_work: 0.3009 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 19541 Z= 0.197 Angle : 0.589 11.889 26534 Z= 0.299 Chirality : 0.047 0.166 3024 Planarity : 0.004 0.048 3374 Dihedral : 5.262 55.626 2616 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 3.36 % Allowed : 19.68 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.17), residues: 2396 helix: -1.01 (0.27), residues: 330 sheet: -0.36 (0.17), residues: 927 loop : -1.65 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 849 TYR 0.021 0.001 TYR B 315 PHE 0.014 0.002 PHE C 217 TRP 0.014 0.001 TRP A1106 HIS 0.006 0.001 HIS A1360 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (19527) covalent geometry : angle 0.58682 / 0.30 (26506) SS BOND : bond 0.00294 / 0.19 ( 14) SS BOND : angle 1.52508 / 0.92 ( 28) hydrogen bonds : bond 0.03256 / 2.09 ( 640) hydrogen bonds : angle 5.07429 / 3.41 ( 1842) *********************** 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 251 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 179 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: C 253 ARG cc_start: 0.7691 (ptp-110) cc_final: 0.7455 (ptt90) REVERT: C 276 LYS cc_start: 0.8402 (mmmt) cc_final: 0.7933 (mptt) REVERT: C 445 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7148 (pm20) REVERT: C 554 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8978 (mt) REVERT: A 796 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8749 (p) REVERT: A 804 ILE cc_start: 0.9056 (mm) cc_final: 0.8815 (mm) REVERT: A 826 GLU cc_start: 0.8226 (pm20) cc_final: 0.7783 (pt0) REVERT: A 917 TRP cc_start: 0.7596 (t-100) cc_final: 0.7275 (m100) REVERT: A 935 LYS cc_start: 0.8669 (ttpt) cc_final: 0.7782 (mttm) REVERT: A 988 LEU cc_start: 0.8912 (mm) cc_final: 0.8645 (mp) REVERT: A 1024 TYR cc_start: 0.7860 (t80) cc_final: 0.7639 (t80) REVERT: A 1161 LEU cc_start: 0.8614 (mm) cc_final: 0.7847 (tt) REVERT: A 1247 MET cc_start: 0.8279 (ttm) cc_final: 0.7926 (ttm) REVERT: B 183 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.6854 (p90) REVERT: B 411 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9072 (pt) REVERT: B 453 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7765 (tm-30) REVERT: B 764 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6961 (tm-30) REVERT: B 811 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7085 (tpt) REVERT: B 1467 LYS cc_start: 0.7981 (mmmm) cc_final: 0.7699 (mmmt) REVERT: B 1481 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7420 (pp) outliers start: 72 outliers final: 55 residues processed: 237 average time/residue: 0.1380 time to fit residues: 52.4576 Evaluate side-chains 236 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 173 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 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 445 GLU 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 833 VAL Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1014 SER Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 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 B residue 86 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 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 492 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 764 GLU 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 1481 LEU Chi-restraints excluded: chain B residue 1482 ASN Chi-restraints excluded: chain B residue 1485 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 124 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 195 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 229 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.121010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098453 restraints weight = 35047.405| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.50 r_work: 0.3049 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19541 Z= 0.120 Angle : 0.538 10.160 26534 Z= 0.274 Chirality : 0.045 0.161 3024 Planarity : 0.004 0.051 3374 Dihedral : 4.991 53.287 2616 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.71 % Allowed : 20.15 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.17), residues: 2396 helix: -0.83 (0.28), residues: 328 sheet: -0.15 (0.17), residues: 918 loop : -1.54 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 63 TYR 0.020 0.001 TYR B 315 PHE 0.014 0.001 PHE B 347 TRP 0.020 0.001 TRP A1106 HIS 0.004 0.001 HIS A1202 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (19527) covalent geometry : angle 0.53679 / 0.27 (26506) SS BOND : bond 0.00252 / 0.17 ( 14) SS BOND : angle 1.22961 / 0.72 ( 28) hydrogen bonds : bond 0.02888 / 1.86 ( 640) hydrogen bonds : angle 4.84530 / 3.27 ( 1842) *********************** 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 245 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 187 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: C 175 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: C 253 ARG cc_start: 0.7675 (ptp-110) cc_final: 0.7374 (ptt90) REVERT: C 276 LYS cc_start: 0.8410 (mmmt) cc_final: 0.7960 (mptt) REVERT: A 796 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8677 (p) REVERT: A 804 ILE cc_start: 0.8969 (mm) cc_final: 0.8713 (mm) REVERT: A 826 GLU cc_start: 0.8132 (pm20) cc_final: 0.7783 (pt0) REVERT: A 917 TRP cc_start: 0.7568 (t-100) cc_final: 0.7260 (m100) REVERT: A 935 LYS cc_start: 0.8644 (ttpt) cc_final: 0.7749 (mttm) REVERT: A 988 LEU cc_start: 0.8886 (mm) cc_final: 0.8615 (mp) REVERT: A 1005 LYS cc_start: 0.8331 (mtpt) cc_final: 0.7921 (mmmm) REVERT: A 1024 TYR cc_start: 0.7821 (t80) cc_final: 0.7576 (t80) REVERT: A 1138 ARG cc_start: 0.8149 (mtm-85) cc_final: 0.7888 (ptp90) REVERT: A 1161 LEU cc_start: 0.8534 (mm) cc_final: 0.7746 (tt) REVERT: A 1247 MET cc_start: 0.8230 (ttm) cc_final: 0.7998 (ttm) REVERT: B 183 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.6778 (p90) REVERT: B 264 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8474 (tt) REVERT: B 411 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.9016 (pt) REVERT: B 453 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7684 (tm-30) REVERT: B 764 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6900 (tm-30) REVERT: B 811 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.6959 (tpt) REVERT: B 1467 LYS cc_start: 0.7976 (mmmm) cc_final: 0.7664 (mmmt) outliers start: 58 outliers final: 44 residues processed: 233 average time/residue: 0.1312 time to fit residues: 49.1530 Evaluate side-chains 227 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 176 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 310 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 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 B residue 86 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 VAL 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 492 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 764 GLU 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 1485 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 115 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 64 optimal weight: 0.2980 chunk 227 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 142 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 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 = 0.3603 r_free = 0.3603 target = 0.123035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100688 restraints weight = 34752.611| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.42 r_work: 0.3099 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19541 Z= 0.096 Angle : 0.520 9.155 26534 Z= 0.264 Chirality : 0.045 0.166 3024 Planarity : 0.004 0.052 3374 Dihedral : 4.644 48.821 2616 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.15 % Allowed : 20.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.17), residues: 2396 helix: -0.54 (0.28), residues: 327 sheet: 0.01 (0.18), residues: 933 loop : -1.37 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 227 TYR 0.021 0.001 TYR B 315 PHE 0.013 0.001 PHE B 347 TRP 0.015 0.001 TRP A1106 HIS 0.003 0.000 HIS A1360 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (19527) covalent geometry : angle 0.51882 / 0.26 (26506) SS BOND : bond 0.00213 / 0.15 ( 14) SS BOND : angle 1.12209 / 0.64 ( 28) hydrogen bonds : bond 0.02734 / 1.76 ( 640) hydrogen bonds : angle 4.64060 / 3.13 ( 1842) *********************** 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 245 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 175 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: C 253 ARG cc_start: 0.7715 (ptp-110) cc_final: 0.7420 (ptt90) REVERT: C 276 LYS cc_start: 0.8416 (mmmt) cc_final: 0.7971 (mptt) REVERT: C 554 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8961 (mt) REVERT: A 804 ILE cc_start: 0.8883 (mm) cc_final: 0.8591 (mm) REVERT: A 826 GLU cc_start: 0.8040 (pm20) cc_final: 0.7716 (pt0) REVERT: A 917 TRP cc_start: 0.7461 (t-100) cc_final: 0.7203 (m100) REVERT: A 1005 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7924 (mmmm) REVERT: A 1024 TYR cc_start: 0.7766 (t80) cc_final: 0.7507 (t80) REVERT: A 1161 LEU cc_start: 0.8445 (mm) cc_final: 0.7607 (tt) REVERT: A 1214 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7448 (mtm-85) REVERT: A 1247 MET cc_start: 0.8210 (ttm) cc_final: 0.7982 (ttm) REVERT: A 1259 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7845 (tt) REVERT: A 1504 GLN cc_start: 0.8625 (pp30) cc_final: 0.7926 (pt0) REVERT: B 183 PHE cc_start: 0.7599 (OUTLIER) cc_final: 0.6679 (p90) REVERT: B 264 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8502 (tt) REVERT: B 453 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7600 (tm-30) REVERT: B 811 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.6912 (tpt) REVERT: B 1467 LYS cc_start: 0.7864 (mmmm) cc_final: 0.7545 (mmmt) outliers start: 46 outliers final: 37 residues processed: 233 average time/residue: 0.1358 time to fit residues: 50.0989 Evaluate side-chains 224 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 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 B residue 86 THR Chi-restraints excluded: chain B residue 96 THR 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 329 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 811 MET Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 1378 THR Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1485 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 111 optimal weight: 0.1980 chunk 113 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.100245 restraints weight = 34916.634| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.47 r_work: 0.3086 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19541 Z= 0.108 Angle : 0.527 9.403 26534 Z= 0.266 Chirality : 0.045 0.153 3024 Planarity : 0.004 0.051 3374 Dihedral : 4.652 47.998 2616 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.19 % Allowed : 21.22 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.17), residues: 2396 helix: -0.42 (0.28), residues: 328 sheet: 0.08 (0.17), residues: 932 loop : -1.30 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1138 TYR 0.022 0.001 TYR B 315 PHE 0.012 0.001 PHE B 347 TRP 0.016 0.001 TRP A1106 HIS 0.003 0.001 HIS A1360 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (19527) covalent geometry : angle 0.52580 / 0.27 (26506) SS BOND : bond 0.00224 / 0.15 ( 14) SS BOND : angle 1.09435 / 0.62 ( 28) hydrogen bonds : bond 0.02770 / 1.79 ( 640) hydrogen bonds : angle 4.61074 / 3.12 ( 1842) ********************** 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 227 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: C 175 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: C 253 ARG cc_start: 0.7711 (ptp-110) cc_final: 0.7432 (ptt90) REVERT: C 267 ILE cc_start: 0.9002 (mm) cc_final: 0.8602 (mt) REVERT: C 554 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8966 (mt) REVERT: A 804 ILE cc_start: 0.8895 (mm) cc_final: 0.8595 (mm) REVERT: A 826 GLU cc_start: 0.8042 (pm20) cc_final: 0.7731 (pt0) REVERT: A 917 TRP cc_start: 0.7492 (t-100) cc_final: 0.7222 (m100) REVERT: A 1005 LYS cc_start: 0.8310 (mtpt) cc_final: 0.7944 (mmmm) REVERT: A 1024 TYR cc_start: 0.7756 (t80) cc_final: 0.7514 (t80) REVERT: A 1161 LEU cc_start: 0.8434 (mm) cc_final: 0.7596 (tt) REVERT: A 1214 ARG cc_start: 0.7825 (ttm170) cc_final: 0.7430 (mtm-85) REVERT: A 1247 MET cc_start: 0.8194 (ttm) cc_final: 0.7986 (ttm) REVERT: A 1259 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7808 (tt) REVERT: A 1280 TYR cc_start: 0.8473 (t80) cc_final: 0.8117 (t80) REVERT: A 1504 GLN cc_start: 0.8622 (pp30) cc_final: 0.7940 (pt0) REVERT: B 183 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.6678 (p90) REVERT: B 264 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8495 (tt) REVERT: B 453 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7644 (tm-30) REVERT: B 811 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.6931 (tpt) REVERT: B 1467 LYS cc_start: 0.7857 (mmmm) cc_final: 0.7545 (mmmt) outliers start: 47 outliers final: 37 residues processed: 218 average time/residue: 0.1194 time to fit residues: 42.2070 Evaluate side-chains 218 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 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 B residue 86 THR Chi-restraints excluded: chain B residue 96 THR 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 346 HIS Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 811 MET Chi-restraints excluded: chain B residue 885 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 206 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.119434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.096826 restraints weight = 35130.605| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.49 r_work: 0.3027 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 19541 Z= 0.188 Angle : 0.584 12.374 26534 Z= 0.295 Chirality : 0.046 0.156 3024 Planarity : 0.004 0.049 3374 Dihedral : 5.039 48.438 2616 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 2.47 % Allowed : 21.13 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.17), residues: 2396 helix: -0.50 (0.28), residues: 331 sheet: -0.11 (0.17), residues: 925 loop : -1.34 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1138 TYR 0.021 0.001 TYR B 315 PHE 0.015 0.001 PHE B 464 TRP 0.017 0.001 TRP A1106 HIS 0.005 0.001 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (19527) covalent geometry : angle 0.58312 / 0.29 (26506) SS BOND : bond 0.00258 / 0.17 ( 14) SS BOND : angle 1.18544 / 0.69 ( 28) hydrogen bonds : bond 0.03148 / 2.01 ( 640) hydrogen bonds : angle 4.88469 / 3.30 ( 1842) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3847.97 seconds wall clock time: 67 minutes 8.55 seconds (4028.55 seconds total)