Starting phenix.real_space_refine on Thu Jun 19 19:59:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qdr_13923/06_2025/7qdr_13923.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qdr_13923/06_2025/7qdr_13923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qdr_13923/06_2025/7qdr_13923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qdr_13923/06_2025/7qdr_13923.map" model { file = "/net/cci-nas-00/data/ceres_data/7qdr_13923/06_2025/7qdr_13923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qdr_13923/06_2025/7qdr_13923.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 107 5.16 5 C 14440 2.51 5 N 3969 2.21 5 O 4302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22818 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9065 Classifications: {'peptide': 1169} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 75, 'TRANS': 1093} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 9007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1212, 9007 Classifications: {'peptide': 1212} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 26, 'TRANS': 1185} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 667 Unresolved non-hydrogen dihedrals: 443 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 6, 'TYR:plan': 11, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 298 Chain: "C" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain: "D" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Time building chain proxies: 13.89, per 1000 atoms: 0.61 Number of scatterers: 22818 At special positions: 0 Unit cell: (179.416, 133.468, 142.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 107 16.00 O 4302 8.00 N 3969 7.00 C 14440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 5.71 Conformation dependent library (CDL) restraints added in 2.9 seconds 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5606 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 23 sheets defined 52.2% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.585A pdb=" N SER A 64 " --> pdb=" O GLN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 removed outlier: 4.304A pdb=" N TRP A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) Proline residue: A 70 - end of helix removed outlier: 3.859A pdb=" N GLY A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.562A pdb=" N LEU A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.648A pdb=" N SER A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 removed outlier: 4.182A pdb=" N ARG A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.814A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 377 removed outlier: 4.536A pdb=" N GLN A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 409 removed outlier: 3.740A pdb=" N SER A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.621A pdb=" N TYR A 427 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 428 " --> pdb=" O VAL A 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 424 through 428' Processing helix chain 'A' and resid 433 through 444 removed outlier: 4.163A pdb=" N TRP A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 514 through 529 removed outlier: 3.820A pdb=" N TYR A 518 " --> pdb=" O HIS A 514 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG A 528 " --> pdb=" O ALA A 524 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 563 removed outlier: 3.917A pdb=" N GLY A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 563 " --> pdb=" O ALA A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 587 removed outlier: 3.843A pdb=" N GLN A 582 " --> pdb=" O ARG A 578 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A 583 " --> pdb=" O CYS A 579 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 609 Processing helix chain 'A' and resid 613 through 617 Processing helix chain 'A' and resid 618 through 631 removed outlier: 3.624A pdb=" N ARG A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 652 removed outlier: 3.682A pdb=" N GLU A 645 " --> pdb=" O PRO A 641 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 669 removed outlier: 4.037A pdb=" N VAL A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 703 removed outlier: 3.626A pdb=" N TYR A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 698 " --> pdb=" O PRO A 694 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 734 removed outlier: 3.952A pdb=" N ARG A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 761 through 768 removed outlier: 4.027A pdb=" N MET A 765 " --> pdb=" O ARG A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 771 No H-bonds generated for 'chain 'A' and resid 769 through 771' Processing helix chain 'A' and resid 772 through 777 Processing helix chain 'A' and resid 778 through 794 removed outlier: 4.235A pdb=" N LYS A 791 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY A 794 " --> pdb=" O THR A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 831 Processing helix chain 'A' and resid 832 through 839 Processing helix chain 'A' and resid 884 through 888 removed outlier: 3.901A pdb=" N ASP A 887 " --> pdb=" O ASP A 884 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 888 " --> pdb=" O PRO A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 884 through 888' Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 936 through 948 removed outlier: 4.261A pdb=" N LYS A 946 " --> pdb=" O GLU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 Processing helix chain 'A' and resid 992 through 1010 Processing helix chain 'A' and resid 1011 through 1012 No H-bonds generated for 'chain 'A' and resid 1011 through 1012' Processing helix chain 'A' and resid 1013 through 1017 Processing helix chain 'A' and resid 1019 through 1044 removed outlier: 3.842A pdb=" N GLN A1023 " --> pdb=" O ARG A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1065 Processing helix chain 'A' and resid 1075 through 1083 removed outlier: 4.147A pdb=" N ALA A1083 " --> pdb=" O ARG A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1097 Processing helix chain 'A' and resid 1099 through 1103 removed outlier: 3.994A pdb=" N THR A1102 " --> pdb=" O ALA A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1113 removed outlier: 4.102A pdb=" N ALA A1109 " --> pdb=" O PRO A1105 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA A1110 " --> pdb=" O GLU A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1116 No H-bonds generated for 'chain 'A' and resid 1114 through 1116' Processing helix chain 'A' and resid 1128 through 1151 removed outlier: 3.901A pdb=" N GLU A1136 " --> pdb=" O LYS A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1163 Processing helix chain 'A' and resid 1169 through 1177 Processing helix chain 'A' and resid 1181 through 1189 removed outlier: 3.667A pdb=" N LEU A1185 " --> pdb=" O PRO A1181 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A1189 " --> pdb=" O LEU A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1204 removed outlier: 3.507A pdb=" N VAL A1196 " --> pdb=" O PRO A1192 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A1197 " --> pdb=" O GLU A1193 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS A1199 " --> pdb=" O LEU A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1218 removed outlier: 3.647A pdb=" N ARG A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A1216 " --> pdb=" O GLY A1212 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1230 removed outlier: 3.533A pdb=" N GLY A1223 " --> pdb=" O GLU A1219 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A1225 " --> pdb=" O VAL A1221 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR A1228 " --> pdb=" O ALA A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1240 Processing helix chain 'B' and resid 354 through 366 Processing helix chain 'B' and resid 369 through 383 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 404 through 416 removed outlier: 4.027A pdb=" N ILE B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 436 Processing helix chain 'B' and resid 438 through 452 removed outlier: 3.596A pdb=" N CYS B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B 446 " --> pdb=" O CYS B 442 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 447 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 removed outlier: 3.611A pdb=" N GLY B 461 " --> pdb=" O HIS B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 Processing helix chain 'B' and resid 496 through 504 Processing helix chain 'B' and resid 509 through 524 removed outlier: 3.673A pdb=" N GLY B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 541 Processing helix chain 'B' and resid 546 through 557 Processing helix chain 'B' and resid 563 through 577 removed outlier: 3.857A pdb=" N ARG B 569 " --> pdb=" O TRP B 565 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA B 577 " --> pdb=" O TYR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 removed outlier: 3.576A pdb=" N ALA B 583 " --> pdb=" O GLN B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 611 removed outlier: 3.530A pdb=" N TRP B 601 " --> pdb=" O ASP B 597 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 627 removed outlier: 3.626A pdb=" N LEU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 645 removed outlier: 3.995A pdb=" N VAL B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 662 removed outlier: 3.781A pdb=" N LYS B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 686 removed outlier: 3.657A pdb=" N ASP B 686 " --> pdb=" O ALA B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 710 removed outlier: 4.056A pdb=" N HIS B 709 " --> pdb=" O CYS B 705 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 726 removed outlier: 4.324A pdb=" N TRP B 717 " --> pdb=" O VAL B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 745 removed outlier: 3.562A pdb=" N LEU B 744 " --> pdb=" O GLY B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 773 removed outlier: 3.794A pdb=" N LEU B 772 " --> pdb=" O ARG B 768 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 796 removed outlier: 3.604A pdb=" N TRP B 779 " --> pdb=" O THR B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 821 Processing helix chain 'B' and resid 824 through 836 removed outlier: 3.666A pdb=" N TRP B 828 " --> pdb=" O ASN B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 857 Processing helix chain 'B' and resid 860 through 874 removed outlier: 3.773A pdb=" N TRP B 864 " --> pdb=" O ASN B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 891 Processing helix chain 'B' and resid 894 through 908 removed outlier: 3.784A pdb=" N TRP B 898 " --> pdb=" O TYR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 925 removed outlier: 3.713A pdb=" N ASN B 924 " --> pdb=" O THR B 920 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET B 925 " --> pdb=" O THR B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 943 removed outlier: 3.538A pdb=" N ASP B 943 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 959 Processing helix chain 'B' and resid 960 through 977 Processing helix chain 'B' and resid 979 through 994 removed outlier: 3.957A pdb=" N PHE B 983 " --> pdb=" O TYR B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1010 removed outlier: 3.560A pdb=" N ALA B 999 " --> pdb=" O LEU B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.636A pdb=" N ASN B1020 " --> pdb=" O GLN B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1045 removed outlier: 3.573A pdb=" N SER B1045 " --> pdb=" O GLN B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1065 Processing helix chain 'B' and resid 1066 through 1080 removed outlier: 3.697A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1100 removed outlier: 3.674A pdb=" N LYS B1100 " --> pdb=" O ILE B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1116 removed outlier: 3.690A pdb=" N ALA B1107 " --> pdb=" O LYS B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1123 through 1135 Processing helix chain 'B' and resid 1139 through 1152 removed outlier: 3.837A pdb=" N HIS B1151 " --> pdb=" O GLU B1147 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B1152 " --> pdb=" O LEU B1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1172 removed outlier: 3.747A pdb=" N GLN B1172 " --> pdb=" O ILE B1168 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1189 Processing helix chain 'B' and resid 1192 through 1206 removed outlier: 3.832A pdb=" N TRP B1196 " --> pdb=" O ASP B1192 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1224 Processing helix chain 'B' and resid 1228 through 1244 Processing helix chain 'B' and resid 1254 through 1266 Processing helix chain 'B' and resid 1269 through 1291 removed outlier: 4.628A pdb=" N TRP B1273 " --> pdb=" O ASP B1269 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B1274 " --> pdb=" O PRO B1270 " (cutoff:3.500A) Processing helix chain 'B' and resid 1299 through 1313 removed outlier: 4.077A pdb=" N ASP B1313 " --> pdb=" O ALA B1309 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1340 Processing helix chain 'B' and resid 1341 through 1356 removed outlier: 3.560A pdb=" N SER B1355 " --> pdb=" O LYS B1351 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN B1356 " --> pdb=" O ASN B1352 " (cutoff:3.500A) Processing helix chain 'B' and resid 1361 through 1371 Processing helix chain 'B' and resid 1382 through 1396 removed outlier: 3.729A pdb=" N ASN B1396 " --> pdb=" O THR B1392 " (cutoff:3.500A) Processing helix chain 'B' and resid 1399 through 1414 removed outlier: 3.679A pdb=" N TRP B1403 " --> pdb=" O SER B1399 " (cutoff:3.500A) Processing helix chain 'B' and resid 1415 through 1433 Processing helix chain 'B' and resid 1436 through 1456 removed outlier: 3.987A pdb=" N ALA B1456 " --> pdb=" O LYS B1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 1462 through 1478 Processing helix chain 'B' and resid 1480 through 1494 Processing helix chain 'B' and resid 1498 through 1511 removed outlier: 3.664A pdb=" N ARG B1502 " --> pdb=" O ALA B1498 " (cutoff:3.500A) Processing helix chain 'B' and resid 1515 through 1533 Processing helix chain 'B' and resid 1535 through 1548 Processing helix chain 'B' and resid 1553 through 1563 removed outlier: 3.959A pdb=" N SER B1563 " --> pdb=" O GLN B1559 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.708A pdb=" N ARG A 20 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA3, first strand: chain 'A' and resid 284 through 285 removed outlier: 6.833A pdb=" N ILE A 285 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N SER A 479 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER A 327 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE A 478 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE A 329 " --> pdb=" O ILE A 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 397 through 398 removed outlier: 7.985A pdb=" N MET A 398 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR A 358 " --> pdb=" O MET A 398 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG A 355 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TRP A 419 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU A 418 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE A 451 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL A 420 " --> pdb=" O ILE A 451 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 383 Processing sheet with id=AA6, first strand: chain 'A' and resid 503 through 505 removed outlier: 3.656A pdb=" N LEU A 717 " --> pdb=" O TYR A 490 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 676 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 569 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA A 661 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL A 571 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLY A 633 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 916 through 920 removed outlier: 3.641A pdb=" N ALA A 855 " --> pdb=" O VAL A 847 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG A 843 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL A 844 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE A 928 " --> pdb=" O VAL A 844 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 846 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 737 through 739 Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 11 removed outlier: 7.047A pdb=" N ILE C 300 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS C 10 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE C 298 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 289 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 19 through 25 removed outlier: 6.076A pdb=" N LYS C 48 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU C 56 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 67 through 72 removed outlier: 3.614A pdb=" N ALA C 79 " --> pdb=" O TRP C 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 113 removed outlier: 3.764A pdb=" N TYR C 142 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLY C 134 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LYS C 140 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 151 through 156 removed outlier: 6.614A pdb=" N GLY C 166 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE C 154 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C 164 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE C 174 " --> pdb=" O HIS C 184 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N HIS C 184 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 196 through 198 Processing sheet with id=AB6, first strand: chain 'C' and resid 213 through 217 removed outlier: 6.079A pdb=" N ILE C 214 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR C 227 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE C 216 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 235 through 240 removed outlier: 3.679A pdb=" N ASN C 237 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS C 268 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP C 260 " --> pdb=" O CYS C 266 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N CYS C 266 " --> pdb=" O ASP C 260 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AB9, first strand: chain 'D' and resid 21 through 25 removed outlier: 3.620A pdb=" N TRP D 58 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS D 48 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU D 56 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 67 through 72 removed outlier: 3.585A pdb=" N SER D 69 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS D 100 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 112 through 113 Processing sheet with id=AC3, first strand: chain 'D' and resid 164 through 166 removed outlier: 3.544A pdb=" N ASN D 173 " --> pdb=" O SER D 165 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE D 174 " --> pdb=" O HIS D 184 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N HIS D 184 " --> pdb=" O ILE D 174 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 196 through 197 Processing sheet with id=AC5, first strand: chain 'D' and resid 235 through 239 removed outlier: 6.891A pdb=" N SER D 250 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL D 238 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL D 248 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL D 256 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS D 268 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP D 260 " --> pdb=" O CYS D 266 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N CYS D 266 " --> pdb=" O ASP D 260 " (cutoff:3.500A) 1125 hydrogen bonds defined for protein. 3276 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.77 Time building geometry restraints manager: 6.84 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: 7593 1.34 - 1.46: 4592 1.46 - 1.58: 10916 1.58 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 23269 Sorted by residual: bond pdb=" CB GLU C 141 " pdb=" CG GLU C 141 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.77e+00 bond pdb=" CB ILE B 968 " pdb=" CG2 ILE B 968 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.53e+00 bond pdb=" CB VAL C 290 " pdb=" CG2 VAL C 290 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.47e+00 bond pdb=" CB CYS B 724 " pdb=" SG CYS B 724 " ideal model delta sigma weight residual 1.808 1.750 0.058 3.30e-02 9.18e+02 3.10e+00 bond pdb=" C VAL B1400 " pdb=" N PRO B1401 " ideal model delta sigma weight residual 1.334 1.374 -0.041 2.34e-02 1.83e+03 3.00e+00 ... (remaining 23264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 31150 2.88 - 5.75: 406 5.75 - 8.63: 35 8.63 - 11.51: 5 11.51 - 14.38: 2 Bond angle restraints: 31598 Sorted by residual: angle pdb=" N PRO B 417 " pdb=" CA PRO B 417 " pdb=" CB PRO B 417 " ideal model delta sigma weight residual 102.65 110.65 -8.00 6.80e-01 2.16e+00 1.38e+02 angle pdb=" N PRO A 162 " pdb=" CA PRO A 162 " pdb=" CB PRO A 162 " ideal model delta sigma weight residual 103.25 111.29 -8.04 1.05e+00 9.07e-01 5.86e+01 angle pdb=" N PRO A 206 " pdb=" CA PRO A 206 " pdb=" CB PRO A 206 " ideal model delta sigma weight residual 103.25 111.23 -7.98 1.05e+00 9.07e-01 5.78e+01 angle pdb=" N PRO B 386 " pdb=" CA PRO B 386 " pdb=" CB PRO B 386 " ideal model delta sigma weight residual 103.25 110.27 -7.02 1.05e+00 9.07e-01 4.47e+01 angle pdb=" C LEU B1374 " pdb=" N LEU B1375 " pdb=" CA LEU B1375 " ideal model delta sigma weight residual 121.54 130.36 -8.82 1.91e+00 2.74e-01 2.13e+01 ... (remaining 31593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 12563 17.75 - 35.49: 1242 35.49 - 53.24: 161 53.24 - 70.99: 23 70.99 - 88.73: 15 Dihedral angle restraints: 14004 sinusoidal: 5326 harmonic: 8678 Sorted by residual: dihedral pdb=" CA LEU A 586 " pdb=" C LEU A 586 " pdb=" N THR A 587 " pdb=" CA THR A 587 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASP D 201 " pdb=" C ASP D 201 " pdb=" N SER D 202 " pdb=" CA SER D 202 " ideal model delta harmonic sigma weight residual -180.00 -153.54 -26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA ARG B 947 " pdb=" C ARG B 947 " pdb=" N GLU B 948 " pdb=" CA GLU B 948 " ideal model delta harmonic sigma weight residual 180.00 154.19 25.81 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 14001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2458 0.044 - 0.089: 884 0.089 - 0.133: 234 0.133 - 0.178: 36 0.178 - 0.222: 7 Chirality restraints: 3619 Sorted by residual: chirality pdb=" CA PRO B 386 " pdb=" N PRO B 386 " pdb=" C PRO B 386 " pdb=" CB PRO B 386 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA HIS B 992 " pdb=" N HIS B 992 " pdb=" C HIS B 992 " pdb=" CB HIS B 992 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA PRO A 206 " pdb=" N PRO A 206 " pdb=" C PRO A 206 " pdb=" CB PRO A 206 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 3616 not shown) Planarity restraints: 4070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 13 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO A 14 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO A 14 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 14 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 155 " 0.059 5.00e-02 4.00e+02 9.03e-02 1.31e+01 pdb=" N PRO A 156 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 516 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C CYS B 516 " 0.056 2.00e-02 2.50e+03 pdb=" O CYS B 516 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR B 517 " -0.019 2.00e-02 2.50e+03 ... (remaining 4067 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 237 2.60 - 3.17: 20216 3.17 - 3.75: 33677 3.75 - 4.32: 44452 4.32 - 4.90: 75412 Nonbonded interactions: 173994 Sorted by model distance: nonbonded pdb=" O THR B1392 " pdb=" OG SER B1395 " model vdw 2.021 3.040 nonbonded pdb=" OH TYR A 358 " pdb=" OD2 ASP A 423 " model vdw 2.098 3.040 nonbonded pdb=" OE1 GLU A 40 " pdb=" NZ LYS B1285 " model vdw 2.122 3.120 nonbonded pdb=" OD1 ASP A1069 " pdb=" N GLU A1070 " model vdw 2.128 3.120 nonbonded pdb=" OH TYR A 554 " pdb=" OD2 ASP A 679 " model vdw 2.131 3.040 ... (remaining 173989 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 54.420 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 : 0.006 0.062 23269 Z= 0.245 Angle : 0.837 14.382 31598 Z= 0.460 Chirality : 0.049 0.222 3619 Planarity : 0.006 0.101 4070 Dihedral : 14.042 88.732 8398 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.92 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.15), residues: 2975 helix: 1.09 (0.14), residues: 1444 sheet: -1.95 (0.27), residues: 314 loop : -3.35 (0.14), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 49 HIS 0.010 0.001 HIS B1187 PHE 0.038 0.002 PHE C 271 TYR 0.028 0.002 TYR B1525 ARG 0.021 0.001 ARG A1001 Details of bonding type rmsd hydrogen bonds : bond 0.15881 ( 1125) hydrogen bonds : angle 5.95617 ( 3276) covalent geometry : bond 0.00574 (23269) covalent geometry : angle 0.83703 (31598) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 2.605 Fit side-chains REVERT: C 12 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7102 (mm-30) REVERT: D 50 ARG cc_start: 0.8499 (mmm160) cc_final: 0.8080 (mmm160) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.3486 time to fit residues: 110.1364 Evaluate side-chains 154 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 151 optimal weight: 0.9980 chunk 120 optimal weight: 8.9990 chunk 232 optimal weight: 0.3980 chunk 90 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 269 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 ASN B 942 GLN B1101 GLN B1253 ASN ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 221 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.142282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.110324 restraints weight = 39311.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.108299 restraints weight = 43312.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.109886 restraints weight = 42803.653| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23269 Z= 0.161 Angle : 0.669 11.036 31598 Z= 0.347 Chirality : 0.043 0.165 3619 Planarity : 0.005 0.069 4070 Dihedral : 5.340 24.355 3199 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 0.89 % Allowed : 10.13 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2975 helix: 1.33 (0.14), residues: 1464 sheet: -1.79 (0.29), residues: 301 loop : -3.11 (0.15), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 47 HIS 0.006 0.001 HIS B1187 PHE 0.018 0.001 PHE B1492 TYR 0.021 0.001 TYR A1244 ARG 0.006 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04992 ( 1125) hydrogen bonds : angle 4.63182 ( 3276) covalent geometry : bond 0.00366 (23269) covalent geometry : angle 0.66876 (31598) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 2.599 Fit side-chains REVERT: B 1415 MET cc_start: 0.7674 (mpp) cc_final: 0.6797 (mpp) REVERT: B 1455 MET cc_start: 0.6791 (mmm) cc_final: 0.6548 (mmm) REVERT: C 139 LYS cc_start: 0.8231 (mmtm) cc_final: 0.7997 (mmtp) REVERT: D 30 GLU cc_start: 0.6552 (pm20) cc_final: 0.6254 (pm20) outliers start: 21 outliers final: 14 residues processed: 190 average time/residue: 0.3490 time to fit residues: 107.0425 Evaluate side-chains 173 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain B residue 974 GLU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain D residue 246 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 162 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 272 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 226 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1101 GLN ** B1529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1558 ASN D 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.140311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107266 restraints weight = 39554.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.105325 restraints weight = 47442.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107217 restraints weight = 44658.286| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23269 Z= 0.223 Angle : 0.679 9.697 31598 Z= 0.352 Chirality : 0.044 0.165 3619 Planarity : 0.005 0.070 4070 Dihedral : 5.334 25.658 3199 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 2.28 % Allowed : 13.17 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.16), residues: 2975 helix: 1.28 (0.14), residues: 1468 sheet: -1.82 (0.29), residues: 314 loop : -3.11 (0.15), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 49 HIS 0.007 0.001 HIS B 848 PHE 0.022 0.002 PHE C 271 TYR 0.027 0.002 TYR A1244 ARG 0.004 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.05433 ( 1125) hydrogen bonds : angle 4.58440 ( 3276) covalent geometry : bond 0.00532 (23269) covalent geometry : angle 0.67896 (31598) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 168 time to evaluate : 2.303 Fit side-chains REVERT: A 307 TRP cc_start: 0.7304 (OUTLIER) cc_final: 0.6182 (m-90) REVERT: A 830 MET cc_start: 0.1617 (OUTLIER) cc_final: 0.1195 (pmm) REVERT: B 1415 MET cc_start: 0.7716 (mpp) cc_final: 0.6788 (mpp) REVERT: B 1423 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7656 (m-10) REVERT: B 1455 MET cc_start: 0.6741 (mmm) cc_final: 0.6486 (mmm) REVERT: D 61 GLU cc_start: 0.8197 (pp20) cc_final: 0.7714 (pp20) outliers start: 54 outliers final: 28 residues processed: 206 average time/residue: 0.3391 time to fit residues: 114.0544 Evaluate side-chains 193 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1409 VAL Chi-restraints excluded: chain B residue 1423 TYR Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 248 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 235 optimal weight: 9.9990 chunk 3 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 239 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1205 GLN B1487 GLN B1529 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.141793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108821 restraints weight = 39886.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.106256 restraints weight = 38834.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.108048 restraints weight = 41983.658| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23269 Z= 0.135 Angle : 0.608 10.107 31598 Z= 0.314 Chirality : 0.041 0.158 3619 Planarity : 0.004 0.063 4070 Dihedral : 5.078 23.754 3199 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 2.28 % Allowed : 14.65 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.16), residues: 2975 helix: 1.50 (0.14), residues: 1466 sheet: -1.80 (0.29), residues: 304 loop : -2.94 (0.16), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 49 HIS 0.004 0.001 HIS C 126 PHE 0.019 0.001 PHE B1492 TYR 0.019 0.001 TYR A1244 ARG 0.005 0.000 ARG A 703 Details of bonding type rmsd hydrogen bonds : bond 0.04364 ( 1125) hydrogen bonds : angle 4.28234 ( 3276) covalent geometry : bond 0.00304 (23269) covalent geometry : angle 0.60775 (31598) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 173 time to evaluate : 2.444 Fit side-chains REVERT: A 830 MET cc_start: 0.1647 (OUTLIER) cc_final: 0.1264 (pmm) REVERT: A 1180 MET cc_start: 0.7218 (ttm) cc_final: 0.7007 (ttm) REVERT: B 1098 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6353 (tm-30) REVERT: B 1181 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7997 (tp40) REVERT: B 1415 MET cc_start: 0.7487 (mpp) cc_final: 0.6631 (mpp) REVERT: B 1423 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7764 (m-10) REVERT: B 1455 MET cc_start: 0.6782 (mmm) cc_final: 0.6503 (mmm) REVERT: D 61 GLU cc_start: 0.8216 (pp20) cc_final: 0.7781 (pp20) REVERT: D 159 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7815 (p0) REVERT: D 237 ASN cc_start: 0.8554 (t0) cc_final: 0.8316 (t0) outliers start: 54 outliers final: 32 residues processed: 216 average time/residue: 0.3373 time to fit residues: 119.4215 Evaluate side-chains 202 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1423 TYR Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1448 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 256 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 44 optimal weight: 7.9990 chunk 249 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 284 optimal weight: 5.9990 chunk 276 optimal weight: 0.3980 chunk 142 optimal weight: 0.9980 chunk 269 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN B 879 GLN B1101 GLN C 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.105773 restraints weight = 39606.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.104787 restraints weight = 40587.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105722 restraints weight = 45216.567| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 0.005 0.043 23269 Z= 0.193 Angle : 0.642 9.665 31598 Z= 0.330 Chirality : 0.043 0.156 3619 Planarity : 0.004 0.063 4070 Dihedral : 5.078 24.407 3199 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 3.25 % Allowed : 15.07 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.16), residues: 2975 helix: 1.47 (0.14), residues: 1468 sheet: -1.72 (0.29), residues: 319 loop : -2.95 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 49 HIS 0.005 0.001 HIS B 848 PHE 0.016 0.001 PHE C 271 TYR 0.028 0.001 TYR A1244 ARG 0.004 0.000 ARG A 703 Details of bonding type rmsd hydrogen bonds : bond 0.04844 ( 1125) hydrogen bonds : angle 4.31078 ( 3276) covalent geometry : bond 0.00460 (23269) covalent geometry : angle 0.64166 (31598) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 167 time to evaluate : 2.607 Fit side-chains REVERT: A 307 TRP cc_start: 0.7392 (OUTLIER) cc_final: 0.6214 (m-90) REVERT: A 830 MET cc_start: 0.1427 (OUTLIER) cc_final: 0.1063 (pmm) REVERT: B 1098 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6410 (tm-30) REVERT: B 1181 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8132 (tm-30) REVERT: B 1381 LEU cc_start: 0.8107 (mm) cc_final: 0.7424 (mt) REVERT: B 1415 MET cc_start: 0.7594 (mpp) cc_final: 0.6852 (mpp) REVERT: B 1423 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7818 (m-10) REVERT: B 1455 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.6486 (mmm) REVERT: C 139 LYS cc_start: 0.8301 (mmtm) cc_final: 0.8040 (mmtp) REVERT: D 159 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7853 (p0) outliers start: 77 outliers final: 50 residues processed: 228 average time/residue: 0.3242 time to fit residues: 121.8690 Evaluate side-chains 218 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 162 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1409 VAL Chi-restraints excluded: chain B residue 1423 TYR Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1455 MET Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 305 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 235 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 290 optimal weight: 3.9990 chunk 176 optimal weight: 0.4980 chunk 286 optimal weight: 0.0670 chunk 229 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 overall best weight: 1.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1253 ASN B1558 ASN D 98 GLN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.139988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.106572 restraints weight = 39258.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.102704 restraints weight = 42463.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104585 restraints weight = 39800.360| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23269 Z= 0.176 Angle : 0.625 9.620 31598 Z= 0.320 Chirality : 0.042 0.158 3619 Planarity : 0.004 0.062 4070 Dihedral : 5.014 23.906 3199 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 3.80 % Allowed : 15.70 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.16), residues: 2975 helix: 1.52 (0.14), residues: 1468 sheet: -1.65 (0.29), residues: 314 loop : -2.90 (0.16), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 49 HIS 0.004 0.001 HIS B 848 PHE 0.022 0.001 PHE B1492 TYR 0.024 0.001 TYR A1244 ARG 0.007 0.000 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.04531 ( 1125) hydrogen bonds : angle 4.21710 ( 3276) covalent geometry : bond 0.00417 (23269) covalent geometry : angle 0.62506 (31598) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 171 time to evaluate : 2.706 Fit side-chains REVERT: A 307 TRP cc_start: 0.7439 (OUTLIER) cc_final: 0.6224 (m-90) REVERT: A 830 MET cc_start: 0.1388 (OUTLIER) cc_final: 0.1080 (pmm) REVERT: A 1045 SER cc_start: 0.8557 (p) cc_final: 0.8311 (p) REVERT: B 696 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.9015 (mm) REVERT: B 1098 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6286 (tm-30) REVERT: B 1181 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8131 (tm-30) REVERT: B 1415 MET cc_start: 0.7426 (mpp) cc_final: 0.6725 (mpp) REVERT: B 1423 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.7893 (m-10) REVERT: B 1455 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.6374 (mmm) REVERT: D 53 ARG cc_start: 0.6834 (mtp-110) cc_final: 0.6315 (ptm160) REVERT: D 159 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7910 (p0) REVERT: D 177 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.6964 (tp) REVERT: D 237 ASN cc_start: 0.8613 (t0) cc_final: 0.8352 (t0) outliers start: 90 outliers final: 61 residues processed: 243 average time/residue: 0.3186 time to fit residues: 128.2193 Evaluate side-chains 231 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 162 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 920 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1395 SER Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1409 VAL Chi-restraints excluded: chain B residue 1423 TYR Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1455 MET Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 305 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 64 optimal weight: 7.9990 chunk 208 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 220 optimal weight: 0.0030 chunk 184 optimal weight: 0.6980 chunk 117 optimal weight: 30.0000 chunk 214 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1101 GLN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.108215 restraints weight = 39525.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105627 restraints weight = 42494.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107743 restraints weight = 41243.663| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23269 Z= 0.179 Angle : 0.628 9.502 31598 Z= 0.322 Chirality : 0.042 0.155 3619 Planarity : 0.004 0.060 4070 Dihedral : 4.989 23.884 3199 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 3.67 % Allowed : 17.52 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 2975 helix: 1.55 (0.14), residues: 1468 sheet: -1.61 (0.29), residues: 324 loop : -2.89 (0.16), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 49 HIS 0.004 0.001 HIS D 299 PHE 0.016 0.001 PHE B1112 TYR 0.025 0.001 TYR A1244 ARG 0.005 0.000 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 1125) hydrogen bonds : angle 4.19017 ( 3276) covalent geometry : bond 0.00424 (23269) covalent geometry : angle 0.62796 (31598) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 170 time to evaluate : 2.741 Fit side-chains REVERT: A 307 TRP cc_start: 0.7390 (OUTLIER) cc_final: 0.6091 (m-90) REVERT: A 586 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8121 (mp) REVERT: A 830 MET cc_start: 0.1507 (OUTLIER) cc_final: 0.1208 (pmm) REVERT: A 1037 MET cc_start: 0.7733 (tpt) cc_final: 0.7485 (tpt) REVERT: A 1045 SER cc_start: 0.8593 (p) cc_final: 0.8339 (p) REVERT: B 696 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8997 (mm) REVERT: B 1098 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6325 (tm-30) REVERT: B 1181 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8143 (tm-30) REVERT: B 1415 MET cc_start: 0.7477 (mpp) cc_final: 0.6778 (mpp) REVERT: B 1423 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7916 (m-10) REVERT: B 1449 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.9022 (tp) REVERT: B 1455 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6382 (mmm) REVERT: D 159 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7879 (p0) REVERT: D 177 ILE cc_start: 0.7283 (OUTLIER) cc_final: 0.6926 (tp) outliers start: 87 outliers final: 66 residues processed: 239 average time/residue: 0.3252 time to fit residues: 128.5407 Evaluate side-chains 235 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 159 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 920 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1395 SER Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1409 VAL Chi-restraints excluded: chain B residue 1423 TYR Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1455 MET Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1555 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 305 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 199 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 121 optimal weight: 40.0000 chunk 190 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 chunk 127 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 chunk 148 optimal weight: 0.5980 chunk 279 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1032 GLN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.142217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109014 restraints weight = 39187.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.106013 restraints weight = 40412.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.108032 restraints weight = 40184.272| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23269 Z= 0.132 Angle : 0.603 11.722 31598 Z= 0.306 Chirality : 0.041 0.168 3619 Planarity : 0.004 0.060 4070 Dihedral : 4.827 22.848 3199 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 3.38 % Allowed : 17.98 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2975 helix: 1.68 (0.14), residues: 1470 sheet: -1.53 (0.29), residues: 324 loop : -2.81 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 49 HIS 0.004 0.001 HIS C 126 PHE 0.023 0.001 PHE B1492 TYR 0.019 0.001 TYR B1525 ARG 0.008 0.000 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 1125) hydrogen bonds : angle 4.01974 ( 3276) covalent geometry : bond 0.00302 (23269) covalent geometry : angle 0.60286 (31598) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 180 time to evaluate : 2.418 Fit side-chains REVERT: A 307 TRP cc_start: 0.7275 (OUTLIER) cc_final: 0.6032 (m-90) REVERT: A 586 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8080 (mp) REVERT: A 830 MET cc_start: 0.1535 (OUTLIER) cc_final: 0.1255 (pmm) REVERT: B 1098 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6326 (tm-30) REVERT: B 1181 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8003 (tm-30) REVERT: B 1342 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8739 (mp) REVERT: B 1415 MET cc_start: 0.7461 (mpp) cc_final: 0.6777 (mpp) REVERT: B 1423 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7891 (m-10) REVERT: B 1455 MET cc_start: 0.6682 (OUTLIER) cc_final: 0.6354 (mmm) REVERT: D 159 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7829 (p0) REVERT: D 177 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.7007 (tp) REVERT: D 237 ASN cc_start: 0.8607 (t0) cc_final: 0.8394 (t0) outliers start: 80 outliers final: 57 residues processed: 241 average time/residue: 0.3244 time to fit residues: 128.4486 Evaluate side-chains 234 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 168 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 920 THR Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1186 VAL Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1342 ILE Chi-restraints excluded: chain B residue 1353 LEU Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1395 SER Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1409 VAL Chi-restraints excluded: chain B residue 1411 GLN Chi-restraints excluded: chain B residue 1423 TYR Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1455 MET Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1555 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 305 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 164 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 233 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 259 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 255 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.105781 restraints weight = 39624.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103324 restraints weight = 42406.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104783 restraints weight = 41362.944| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23269 Z= 0.212 Angle : 0.661 10.947 31598 Z= 0.336 Chirality : 0.044 0.200 3619 Planarity : 0.004 0.060 4070 Dihedral : 4.977 24.325 3199 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 3.67 % Allowed : 18.24 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2975 helix: 1.56 (0.14), residues: 1463 sheet: -1.60 (0.29), residues: 324 loop : -2.85 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 49 HIS 0.005 0.001 HIS B 848 PHE 0.021 0.002 PHE B1112 TYR 0.026 0.001 TYR A1244 ARG 0.009 0.000 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.04836 ( 1125) hydrogen bonds : angle 4.21227 ( 3276) covalent geometry : bond 0.00509 (23269) covalent geometry : angle 0.66061 (31598) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 158 time to evaluate : 2.458 Fit side-chains REVERT: A 307 TRP cc_start: 0.7458 (OUTLIER) cc_final: 0.6091 (m-90) REVERT: A 586 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8114 (mp) REVERT: A 830 MET cc_start: 0.1642 (OUTLIER) cc_final: 0.1411 (pmm) REVERT: A 1045 SER cc_start: 0.8631 (p) cc_final: 0.8364 (p) REVERT: B 696 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.9009 (mm) REVERT: B 1098 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6434 (tm-30) REVERT: B 1342 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8818 (mp) REVERT: B 1415 MET cc_start: 0.7531 (mpp) cc_final: 0.6862 (mpp) REVERT: B 1423 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7898 (m-10) REVERT: B 1455 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6406 (mmm) REVERT: B 1479 PHE cc_start: 0.7250 (t80) cc_final: 0.7044 (t80) REVERT: D 53 ARG cc_start: 0.6613 (mtp-110) cc_final: 0.6124 (ptm160) REVERT: D 177 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.7005 (tp) outliers start: 87 outliers final: 69 residues processed: 230 average time/residue: 0.3213 time to fit residues: 122.2467 Evaluate side-chains 236 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 158 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 920 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1342 ILE Chi-restraints excluded: chain B residue 1353 LEU Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1395 SER Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1409 VAL Chi-restraints excluded: chain B residue 1411 GLN Chi-restraints excluded: chain B residue 1423 TYR Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1455 MET Chi-restraints excluded: chain B residue 1489 LEU Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1555 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 305 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 13 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 276 optimal weight: 0.4980 chunk 194 optimal weight: 0.9990 chunk 203 optimal weight: 0.7980 chunk 190 optimal weight: 0.2980 chunk 85 optimal weight: 0.1980 chunk 295 optimal weight: 4.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 847 GLN B1101 GLN B1352 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.143656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.110528 restraints weight = 39428.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.107123 restraints weight = 41841.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109046 restraints weight = 38172.215| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23269 Z= 0.114 Angle : 0.609 10.779 31598 Z= 0.307 Chirality : 0.041 0.219 3619 Planarity : 0.004 0.063 4070 Dihedral : 4.743 24.550 3199 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 2.62 % Allowed : 19.33 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.16), residues: 2975 helix: 1.74 (0.14), residues: 1469 sheet: -1.41 (0.29), residues: 320 loop : -2.74 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B1524 HIS 0.005 0.001 HIS C 126 PHE 0.025 0.001 PHE B1492 TYR 0.018 0.001 TYR B1525 ARG 0.008 0.000 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 1125) hydrogen bonds : angle 3.91403 ( 3276) covalent geometry : bond 0.00249 (23269) covalent geometry : angle 0.60926 (31598) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 170 time to evaluate : 3.337 Fit side-chains REVERT: A 17 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6431 (tp) REVERT: A 307 TRP cc_start: 0.7240 (OUTLIER) cc_final: 0.5926 (m-90) REVERT: A 586 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8135 (mp) REVERT: A 786 LEU cc_start: 0.7934 (tp) cc_final: 0.7708 (tp) REVERT: A 830 MET cc_start: 0.1681 (OUTLIER) cc_final: 0.1467 (pmm) REVERT: B 1098 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6368 (tm-30) REVERT: B 1181 GLN cc_start: 0.8248 (tm-30) cc_final: 0.8024 (tp40) REVERT: B 1342 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8614 (mp) REVERT: B 1415 MET cc_start: 0.7329 (mpp) cc_final: 0.6620 (mpp) REVERT: B 1423 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7892 (m-10) REVERT: B 1455 MET cc_start: 0.6808 (mmm) cc_final: 0.6490 (mmm) outliers start: 62 outliers final: 45 residues processed: 217 average time/residue: 0.3193 time to fit residues: 114.7572 Evaluate side-chains 216 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 164 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1342 ILE Chi-restraints excluded: chain B residue 1353 LEU Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1395 SER Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1411 GLN Chi-restraints excluded: chain B residue 1423 TYR Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1489 LEU Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1555 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 305 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 151 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 259 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 129 optimal weight: 7.9990 chunk 224 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 257 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.143130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.109927 restraints weight = 39543.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108362 restraints weight = 39338.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.109721 restraints weight = 42460.964| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23269 Z= 0.122 Angle : 0.604 10.234 31598 Z= 0.304 Chirality : 0.041 0.219 3619 Planarity : 0.004 0.056 4070 Dihedral : 4.641 23.803 3199 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 2.70 % Allowed : 19.46 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 2975 helix: 1.81 (0.14), residues: 1469 sheet: -1.39 (0.29), residues: 320 loop : -2.68 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B1524 HIS 0.004 0.001 HIS C 126 PHE 0.023 0.001 PHE B1479 TYR 0.017 0.001 TYR B1525 ARG 0.008 0.000 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 1125) hydrogen bonds : angle 3.87490 ( 3276) covalent geometry : bond 0.00276 (23269) covalent geometry : angle 0.60383 (31598) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6352.10 seconds wall clock time: 113 minutes 3.85 seconds (6783.85 seconds total)