Starting phenix.real_space_refine on Thu Mar 5 13:49:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qdr_13923/03_2026/7qdr_13923.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qdr_13923/03_2026/7qdr_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 { model { file = "/net/cci-nas-00/data/ceres_data/7qdr_13923/03_2026/7qdr_13923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qdr_13923/03_2026/7qdr_13923.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qdr_13923/03_2026/7qdr_13923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qdr_13923/03_2026/7qdr_13923.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ASP:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3} 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: {'HIS:plan': 6, 'GLU:plan': 13, 'ASP:plan': 14, 'TYR:plan': 11, 'ARG:plan': 6, 'GLN:plan1': 4, 'ASN:plan1': 2, 'PHE:plan': 6, 'TRP:plan': 1} 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: 4.56, per 1000 atoms: 0.20 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: 1.66 Conformation dependent library (CDL) restraints added in 1.0 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: 0.82 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: 4.53 Time building geometry restraints manager: 2.24 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: 4.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.610 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.220 ------------------------------------------------------------------------------- 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 : 12.57 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (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 ARG 0.021 0.001 ARG A1001 TYR 0.028 0.002 TYR B1525 PHE 0.038 0.002 PHE C 271 TRP 0.029 0.002 TRP D 49 HIS 0.010 0.001 HIS B1187 Details of bonding type rmsd covalent geometry : bond 0.00574 (23269) covalent geometry : angle 0.83703 (31598) hydrogen bonds : bond 0.15881 ( 1125) hydrogen bonds : angle 5.95617 ( 3276) *********************** 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 : 0.769 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: 0.1402 time to fit residues: 44.5722 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 : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.0570 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.1980 overall best weight: 0.8502 ------------------------------------------------------------------------------- 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 C 57 GLN D 3 ASN D 98 GLN D 221 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.142674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.109751 restraints weight = 39544.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108097 restraints weight = 42380.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.109776 restraints weight = 41334.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110019 restraints weight = 25189.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110678 restraints weight = 23474.632| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23269 Z= 0.152 Angle : 0.666 11.018 31598 Z= 0.345 Chirality : 0.043 0.164 3619 Planarity : 0.005 0.069 4070 Dihedral : 5.341 24.371 3199 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 0.93 % Allowed : 9.84 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.16), residues: 2975 helix: 1.33 (0.14), residues: 1465 sheet: -1.77 (0.29), residues: 301 loop : -3.10 (0.15), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 20 TYR 0.020 0.001 TYR A1244 PHE 0.018 0.001 PHE B1492 TRP 0.017 0.001 TRP C 47 HIS 0.006 0.001 HIS B1187 Details of bonding type rmsd covalent geometry : bond 0.00342 (23269) covalent geometry : angle 0.66617 (31598) hydrogen bonds : bond 0.05030 ( 1125) hydrogen bonds : angle 4.64296 ( 3276) *********************** 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 198 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.809 Fit side-chains REVERT: B 1283 ASP cc_start: 0.7666 (t0) cc_final: 0.7464 (t0) REVERT: B 1338 ASP cc_start: 0.7166 (t0) cc_final: 0.6900 (t0) REVERT: B 1415 MET cc_start: 0.7581 (mpp) cc_final: 0.6673 (mpp) REVERT: B 1455 MET cc_start: 0.6836 (mmm) cc_final: 0.6548 (mmm) REVERT: C 139 LYS cc_start: 0.8217 (mmtm) cc_final: 0.7978 (mmtp) REVERT: D 50 ARG cc_start: 0.8407 (mmm160) cc_final: 0.8187 (mmm-85) REVERT: D 91 TRP cc_start: 0.8633 (m100) cc_final: 0.8394 (m100) outliers start: 22 outliers final: 14 residues processed: 189 average time/residue: 0.1426 time to fit residues: 43.4440 Evaluate side-chains 175 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 76 optimal weight: 9.9990 chunk 276 optimal weight: 0.2980 chunk 81 optimal weight: 0.0770 chunk 239 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 289 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1101 GLN B1529 HIS B1558 ASN ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.142751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.109575 restraints weight = 39700.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106211 restraints weight = 41855.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107955 restraints weight = 39684.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108395 restraints weight = 25746.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108665 restraints weight = 23775.556| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23269 Z= 0.157 Angle : 0.632 9.823 31598 Z= 0.326 Chirality : 0.042 0.161 3619 Planarity : 0.005 0.065 4070 Dihedral : 5.171 24.456 3199 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 1.73 % Allowed : 12.49 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.16), residues: 2975 helix: 1.43 (0.14), residues: 1466 sheet: -1.74 (0.29), residues: 304 loop : -3.01 (0.15), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 703 TYR 0.019 0.001 TYR A1244 PHE 0.015 0.001 PHE C 247 TRP 0.014 0.001 TRP C 47 HIS 0.005 0.001 HIS B 848 Details of bonding type rmsd covalent geometry : bond 0.00363 (23269) covalent geometry : angle 0.63162 (31598) hydrogen bonds : bond 0.04681 ( 1125) hydrogen bonds : angle 4.41448 ( 3276) *********************** 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 219 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.859 Fit side-chains REVERT: A 830 MET cc_start: 0.1298 (OUTLIER) cc_final: 0.0925 (pmm) REVERT: B 1181 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8096 (tp40) REVERT: B 1338 ASP cc_start: 0.7181 (t0) cc_final: 0.6925 (t0) REVERT: B 1411 GLN cc_start: 0.8493 (tt0) cc_final: 0.8259 (tt0) REVERT: B 1415 MET cc_start: 0.7444 (mpp) cc_final: 0.6378 (mpp) REVERT: B 1423 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7625 (m-10) REVERT: B 1455 MET cc_start: 0.6932 (mmm) cc_final: 0.6595 (mmm) REVERT: D 61 GLU cc_start: 0.8127 (pp20) cc_final: 0.7597 (pp20) outliers start: 41 outliers final: 20 residues processed: 207 average time/residue: 0.1352 time to fit residues: 45.8930 Evaluate side-chains 184 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 406 MET 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 974 GLU 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 1289 VAL Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1375 LEU 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 275 ASP Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 303 CYS 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 229 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 71 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 293 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 B1101 GLN B1205 GLN B1487 GLN C 285 ASN D 3 ASN D 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106560 restraints weight = 39971.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.104499 restraints weight = 42128.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106230 restraints weight = 44667.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.106489 restraints weight = 25915.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107750 restraints weight = 23676.793| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23269 Z= 0.227 Angle : 0.670 10.030 31598 Z= 0.345 Chirality : 0.044 0.162 3619 Planarity : 0.005 0.066 4070 Dihedral : 5.202 24.883 3199 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 3.04 % Allowed : 14.01 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.16), residues: 2975 helix: 1.35 (0.14), residues: 1468 sheet: -1.87 (0.29), residues: 304 loop : -3.00 (0.15), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 703 TYR 0.029 0.002 TYR A1244 PHE 0.022 0.002 PHE B1492 TRP 0.016 0.001 TRP D 49 HIS 0.007 0.001 HIS B 848 Details of bonding type rmsd covalent geometry : bond 0.00544 (23269) covalent geometry : angle 0.67008 (31598) hydrogen bonds : bond 0.05269 ( 1125) hydrogen bonds : angle 4.47612 ( 3276) *********************** 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 241 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 169 time to evaluate : 0.870 Fit side-chains REVERT: A 307 TRP cc_start: 0.7263 (OUTLIER) cc_final: 0.6093 (m-90) REVERT: A 830 MET cc_start: 0.1570 (OUTLIER) cc_final: 0.1174 (pmm) REVERT: B 1415 MET cc_start: 0.7710 (mpp) cc_final: 0.6970 (mpp) REVERT: B 1423 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.7786 (m-10) REVERT: B 1455 MET cc_start: 0.6868 (mmm) cc_final: 0.6595 (mmm) REVERT: C 139 LYS cc_start: 0.8300 (mmtm) cc_final: 0.7969 (mmtp) REVERT: D 49 TRP cc_start: 0.7739 (t-100) cc_final: 0.7526 (t-100) REVERT: D 61 GLU cc_start: 0.8175 (pp20) cc_final: 0.7808 (pp20) REVERT: D 159 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7831 (p0) outliers start: 72 outliers final: 40 residues processed: 224 average time/residue: 0.1387 time to fit residues: 51.2956 Evaluate side-chains 203 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 307 TRP 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 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 973 VAL 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 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 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 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 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 192 optimal weight: 0.8980 chunk 275 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 chunk 274 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 249 optimal weight: 0.9980 chunk 276 optimal weight: 0.9980 chunk 246 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: B1101 GLN B1253 ASN B1413 GLN D 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.141710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.109231 restraints weight = 39561.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.108420 restraints weight = 41095.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.109404 restraints weight = 45183.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.109802 restraints weight = 26747.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.110784 restraints weight = 23912.297| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23269 Z= 0.147 Angle : 0.610 9.833 31598 Z= 0.314 Chirality : 0.042 0.158 3619 Planarity : 0.004 0.065 4070 Dihedral : 5.014 23.600 3199 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 2.91 % Allowed : 14.99 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.16), residues: 2975 helix: 1.54 (0.14), residues: 1469 sheet: -1.72 (0.28), residues: 324 loop : -2.94 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 703 TYR 0.021 0.001 TYR A1244 PHE 0.014 0.001 PHE C 247 TRP 0.012 0.001 TRP B 936 HIS 0.004 0.001 HIS D 299 Details of bonding type rmsd covalent geometry : bond 0.00342 (23269) covalent geometry : angle 0.60980 (31598) hydrogen bonds : bond 0.04282 ( 1125) hydrogen bonds : angle 4.20356 ( 3276) *********************** 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 236 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 167 time to evaluate : 0.784 Fit side-chains REVERT: A 307 TRP cc_start: 0.7321 (OUTLIER) cc_final: 0.6150 (m-90) REVERT: A 830 MET cc_start: 0.1701 (OUTLIER) cc_final: 0.1342 (pmm) REVERT: B 1181 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7970 (tp40) REVERT: B 1415 MET cc_start: 0.7509 (mpp) cc_final: 0.6761 (mpp) REVERT: B 1423 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7769 (m-10) REVERT: C 139 LYS cc_start: 0.8379 (mmtm) cc_final: 0.7995 (mmtp) REVERT: D 159 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7764 (p0) REVERT: D 237 ASN cc_start: 0.8579 (t0) cc_final: 0.8330 (t0) outliers start: 69 outliers final: 43 residues processed: 222 average time/residue: 0.1357 time to fit residues: 49.7668 Evaluate side-chains 208 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 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 112 LEU 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 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 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 233 optimal weight: 7.9990 chunk 296 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 64 optimal weight: 0.2980 chunk 138 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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** B 879 GLN B1101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.139313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.106285 restraints weight = 39728.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.104945 restraints weight = 44606.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106347 restraints weight = 45051.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.106714 restraints weight = 27836.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.107559 restraints weight = 25837.913| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 23269 Z= 0.231 Angle : 0.663 9.788 31598 Z= 0.341 Chirality : 0.044 0.159 3619 Planarity : 0.005 0.066 4070 Dihedral : 5.098 24.680 3199 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 3.63 % Allowed : 15.53 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.16), residues: 2975 helix: 1.42 (0.14), residues: 1468 sheet: -1.73 (0.28), residues: 334 loop : -2.98 (0.16), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.030 0.002 TYR A1244 PHE 0.023 0.002 PHE B1492 TRP 0.019 0.001 TRP D 49 HIS 0.006 0.001 HIS B 848 Details of bonding type rmsd covalent geometry : bond 0.00553 (23269) covalent geometry : angle 0.66255 (31598) hydrogen bonds : bond 0.05107 ( 1125) hydrogen bonds : angle 4.36137 ( 3276) *********************** 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 250 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 164 time to evaluate : 0.632 Fit side-chains REVERT: A 307 TRP cc_start: 0.7414 (OUTLIER) cc_final: 0.6183 (m-90) REVERT: A 830 MET cc_start: 0.1750 (OUTLIER) cc_final: 0.1372 (pmm) REVERT: A 1045 SER cc_start: 0.8614 (p) cc_final: 0.8361 (p) REVERT: B 696 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.9008 (mm) REVERT: B 1415 MET cc_start: 0.7581 (mpp) cc_final: 0.6987 (mpp) REVERT: B 1423 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7906 (m-10) REVERT: D 159 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7808 (p0) REVERT: D 177 ILE cc_start: 0.7252 (OUTLIER) cc_final: 0.6911 (tp) outliers start: 86 outliers final: 63 residues processed: 237 average time/residue: 0.1264 time to fit residues: 49.8541 Evaluate side-chains 229 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 160 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 400 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 506 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 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 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 1353 LEU 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 1462 HIS Chi-restraints excluded: chain C residue 36 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 38 optimal weight: 0.6980 chunk 223 optimal weight: 6.9990 chunk 114 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 205 optimal weight: 7.9990 chunk 122 optimal weight: 0.5980 chunk 265 optimal weight: 0.6980 chunk 191 optimal weight: 4.9990 chunk 119 optimal weight: 50.0000 chunk 261 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1032 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.143030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.109984 restraints weight = 39490.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107674 restraints weight = 41117.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109590 restraints weight = 40025.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.109512 restraints weight = 25501.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.110026 restraints weight = 23838.957| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1912 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= 0.119 Angle : 0.595 13.202 31598 Z= 0.303 Chirality : 0.041 0.166 3619 Planarity : 0.004 0.063 4070 Dihedral : 4.827 22.292 3199 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 2.70 % Allowed : 17.98 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.16), residues: 2975 helix: 1.65 (0.14), residues: 1473 sheet: -1.45 (0.29), residues: 320 loop : -2.84 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 53 TYR 0.022 0.001 TYR B1525 PHE 0.013 0.001 PHE C 247 TRP 0.020 0.001 TRP D 49 HIS 0.004 0.001 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00262 (23269) covalent geometry : angle 0.59513 (31598) hydrogen bonds : bond 0.03756 ( 1125) hydrogen bonds : angle 4.00735 ( 3276) *********************** 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 248 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 184 time to evaluate : 0.806 Fit side-chains REVERT: A 307 TRP cc_start: 0.7320 (OUTLIER) cc_final: 0.6097 (m-90) REVERT: A 763 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: A 830 MET cc_start: 0.1621 (OUTLIER) cc_final: 0.1315 (pmm) REVERT: B 1181 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7982 (tp40) REVERT: B 1415 MET cc_start: 0.7409 (mpp) cc_final: 0.6747 (mpp) REVERT: B 1423 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7794 (m-10) REVERT: D 53 ARG cc_start: 0.6578 (mtp-110) cc_final: 0.6132 (ptm160) REVERT: D 159 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7803 (p0) REVERT: D 237 ASN cc_start: 0.8567 (t0) cc_final: 0.8353 (t0) outliers start: 64 outliers final: 44 residues processed: 233 average time/residue: 0.1287 time to fit residues: 49.2907 Evaluate side-chains 218 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 86 ASP 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 572 PHE 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 763 GLU 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 645 LEU Chi-restraints excluded: chain B residue 665 TYR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 949 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 1101 GLN Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1353 LEU Chi-restraints excluded: chain B residue 1375 LEU 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 C residue 36 VAL Chi-restraints excluded: chain C residue 112 LEU 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 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 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 212 optimal weight: 0.7980 chunk 251 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 chunk 24 optimal weight: 0.0270 chunk 26 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.143125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.110013 restraints weight = 39158.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106819 restraints weight = 42753.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108519 restraints weight = 39679.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109123 restraints weight = 25476.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109254 restraints weight = 23982.021| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23269 Z= 0.126 Angle : 0.595 12.091 31598 Z= 0.301 Chirality : 0.041 0.220 3619 Planarity : 0.004 0.058 4070 Dihedral : 4.693 22.057 3199 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 2.83 % Allowed : 18.40 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 2975 helix: 1.73 (0.14), residues: 1472 sheet: -1.42 (0.29), residues: 322 loop : -2.77 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 53 TYR 0.018 0.001 TYR B1525 PHE 0.024 0.001 PHE B1492 TRP 0.021 0.001 TRP D 49 HIS 0.004 0.001 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00285 (23269) covalent geometry : angle 0.59475 (31598) hydrogen bonds : bond 0.03761 ( 1125) hydrogen bonds : angle 3.93330 ( 3276) *********************** 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 243 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 176 time to evaluate : 0.747 Fit side-chains REVERT: A 307 TRP cc_start: 0.7256 (OUTLIER) cc_final: 0.6021 (m-90) REVERT: A 586 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8096 (mp) REVERT: A 763 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: A 830 MET cc_start: 0.1559 (OUTLIER) cc_final: 0.1311 (pmm) REVERT: B 1181 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7970 (tp40) REVERT: B 1415 MET cc_start: 0.7378 (mpp) cc_final: 0.6713 (mpp) REVERT: B 1423 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.7820 (m-10) REVERT: D 159 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7839 (p0) REVERT: D 177 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.6991 (tp) REVERT: D 237 ASN cc_start: 0.8576 (t0) cc_final: 0.8372 (t0) outliers start: 67 outliers final: 47 residues processed: 230 average time/residue: 0.1307 time to fit residues: 50.1837 Evaluate side-chains 225 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 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 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 689 PHE Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 763 GLU 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 1186 VAL Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1353 LEU 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 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 269 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 67 VAL 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 180 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 246 optimal weight: 0.9980 chunk 285 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 155 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.143887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.110389 restraints weight = 39677.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.108725 restraints weight = 37702.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.109943 restraints weight = 43935.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110138 restraints weight = 26655.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111188 restraints weight = 23335.108| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23269 Z= 0.116 Angle : 0.592 13.126 31598 Z= 0.297 Chirality : 0.041 0.273 3619 Planarity : 0.004 0.060 4070 Dihedral : 4.561 21.450 3199 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 2.62 % Allowed : 18.95 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.16), residues: 2975 helix: 1.81 (0.14), residues: 1475 sheet: -1.35 (0.30), residues: 315 loop : -2.68 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 53 TYR 0.014 0.001 TYR B1525 PHE 0.020 0.001 PHE B1479 TRP 0.033 0.001 TRP D 49 HIS 0.004 0.001 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00259 (23269) covalent geometry : angle 0.59177 (31598) hydrogen bonds : bond 0.03486 ( 1125) hydrogen bonds : angle 3.83036 ( 3276) *********************** 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 247 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 185 time to evaluate : 0.748 Fit side-chains REVERT: A 17 LEU cc_start: 0.6895 (mp) cc_final: 0.6233 (tp) REVERT: A 307 TRP cc_start: 0.7201 (OUTLIER) cc_final: 0.5911 (m-90) REVERT: A 586 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8138 (mp) REVERT: A 763 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: A 830 MET cc_start: 0.1612 (OUTLIER) cc_final: 0.1392 (pmm) REVERT: B 1181 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7964 (tp40) REVERT: B 1411 GLN cc_start: 0.8486 (pt0) cc_final: 0.8261 (pt0) REVERT: B 1415 MET cc_start: 0.7311 (mpp) cc_final: 0.6570 (mpp) REVERT: B 1423 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7752 (m-10) REVERT: B 1455 MET cc_start: 0.6592 (mmm) cc_final: 0.6234 (mmm) REVERT: D 53 ARG cc_start: 0.6478 (mtp-110) cc_final: 0.6037 (ptm160) REVERT: D 61 GLU cc_start: 0.8228 (pp20) cc_final: 0.7918 (pt0) REVERT: D 159 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7911 (p0) REVERT: D 177 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.6979 (tp) REVERT: D 237 ASN cc_start: 0.8572 (t0) cc_final: 0.8337 (t0) outliers start: 62 outliers final: 44 residues processed: 235 average time/residue: 0.1299 time to fit residues: 50.7000 Evaluate side-chains 225 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 174 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR 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 400 THR 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 656 VAL Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 763 GLU 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 1029 LEU Chi-restraints excluded: chain B residue 1186 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 1353 LEU 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 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 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 251 SER 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 279 optimal weight: 0.5980 chunk 209 optimal weight: 0.8980 chunk 282 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 23 optimal weight: 0.0040 chunk 180 optimal weight: 0.6980 chunk 254 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 247 optimal weight: 0.0070 chunk 245 optimal weight: 0.8980 overall best weight: 0.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.144992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112087 restraints weight = 39358.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.109249 restraints weight = 41700.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.110777 restraints weight = 39764.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.111357 restraints weight = 25301.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111510 restraints weight = 23752.984| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23269 Z= 0.108 Angle : 0.585 10.917 31598 Z= 0.294 Chirality : 0.040 0.206 3619 Planarity : 0.004 0.056 4070 Dihedral : 4.443 20.388 3199 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 2.20 % Allowed : 19.33 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 2975 helix: 1.87 (0.14), residues: 1480 sheet: -1.34 (0.30), residues: 303 loop : -2.61 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 53 TYR 0.015 0.001 TYR B1525 PHE 0.024 0.001 PHE B1492 TRP 0.026 0.001 TRP B1524 HIS 0.004 0.001 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00237 (23269) covalent geometry : angle 0.58460 (31598) hydrogen bonds : bond 0.03273 ( 1125) hydrogen bonds : angle 3.74160 ( 3276) ********************** 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 239 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 0.819 Fit side-chains REVERT: A 17 LEU cc_start: 0.6667 (mp) cc_final: 0.6121 (tp) REVERT: A 307 TRP cc_start: 0.7286 (OUTLIER) cc_final: 0.5958 (m-90) REVERT: A 763 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: A 830 MET cc_start: 0.1769 (OUTLIER) cc_final: 0.1557 (pmm) REVERT: B 1181 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7941 (tp40) REVERT: B 1411 GLN cc_start: 0.8512 (pt0) cc_final: 0.8293 (pt0) REVERT: B 1415 MET cc_start: 0.7246 (mpp) cc_final: 0.6545 (mpp) REVERT: B 1423 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7707 (m-10) REVERT: B 1455 MET cc_start: 0.6596 (mmm) cc_final: 0.6279 (mmm) REVERT: D 53 ARG cc_start: 0.6378 (mtp-110) cc_final: 0.6034 (ptm160) REVERT: D 61 GLU cc_start: 0.8229 (pp20) cc_final: 0.7970 (pt0) REVERT: D 159 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7910 (p0) REVERT: D 177 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.6903 (tp) REVERT: D 223 ASN cc_start: 0.7975 (p0) cc_final: 0.7720 (p0) outliers start: 52 outliers final: 41 residues processed: 228 average time/residue: 0.1330 time to fit residues: 50.3333 Evaluate side-chains 218 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR 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 400 THR 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 763 GLU 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 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 1029 LEU Chi-restraints excluded: chain B residue 1186 VAL Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1311 ILE Chi-restraints excluded: chain B residue 1353 LEU 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 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 177 ILE Chi-restraints excluded: chain D residue 189 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 221 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 262 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 241 optimal weight: 1.9990 chunk 291 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 209 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.143248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.109948 restraints weight = 39337.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107845 restraints weight = 38165.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.109446 restraints weight = 41436.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.109572 restraints weight = 25618.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.110948 restraints weight = 23428.582| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23269 Z= 0.137 Angle : 0.604 10.784 31598 Z= 0.304 Chirality : 0.041 0.207 3619 Planarity : 0.004 0.059 4070 Dihedral : 4.478 21.496 3199 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 2.62 % Allowed : 18.83 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.16), residues: 2975 helix: 1.88 (0.14), residues: 1476 sheet: -1.39 (0.29), residues: 317 loop : -2.66 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 53 TYR 0.017 0.001 TYR A1244 PHE 0.013 0.001 PHE C 247 TRP 0.026 0.001 TRP B1524 HIS 0.003 0.001 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00320 (23269) covalent geometry : angle 0.60374 (31598) hydrogen bonds : bond 0.03753 ( 1125) hydrogen bonds : angle 3.80264 ( 3276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2853.50 seconds wall clock time: 50 minutes 33.16 seconds (3033.16 seconds total)