Starting phenix.real_space_refine on Wed Jun 11 02:15:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asp_43822/06_2025/9asp_43822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asp_43822/06_2025/9asp_43822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9asp_43822/06_2025/9asp_43822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asp_43822/06_2025/9asp_43822.map" model { file = "/net/cci-nas-00/data/ceres_data/9asp_43822/06_2025/9asp_43822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asp_43822/06_2025/9asp_43822.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 P 96 5.49 5 S 64 5.16 5 C 7386 2.51 5 N 2145 2.21 5 O 2532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12227 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7468 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 861} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1990 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 239} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 729 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "E" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 2035 Classifications: {'RNA': 96} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 40, 'rna3p_pyr': 42} Link IDs: {'rna2p': 13, 'rna3p': 82} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 955 SG CYS A 561 42.918 81.838 148.452 1.00172.12 S ATOM 1913 SG CYS A 676 45.995 79.463 148.191 1.00178.36 S ATOM 763 SG CYS A 536 61.773 62.441 134.035 1.00181.72 S ATOM 778 SG CYS A 538 62.519 61.043 130.484 1.00190.39 S Time building chain proxies: 7.48, per 1000 atoms: 0.61 Number of scatterers: 12227 At special positions: 0 Unit cell: (90.2, 103.4, 194.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 2 19.99 S 64 16.00 P 96 15.00 O 2532 8.00 N 2145 7.00 C 7386 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: 2.81 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 609 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 680 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 676 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 561 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" NE2 HIS A1026 " pdb="ZN ZN A1402 " - pdb=" NE2 HIS A 549 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 536 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 538 " Number of angles added : 4 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 53.7% alpha, 10.9% beta 32 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'A' and resid 439 through 452 removed outlier: 4.631A pdb=" N ASP A 446 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 462 removed outlier: 3.721A pdb=" N ALA A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 512 Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.639A pdb=" N THR A 545 " --> pdb=" O ALA A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 655 Processing helix chain 'A' and resid 698 through 709 removed outlier: 3.625A pdb=" N ILE A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 Processing helix chain 'A' and resid 726 through 737 removed outlier: 3.816A pdb=" N CYS A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 786 Processing helix chain 'A' and resid 787 through 806 removed outlier: 3.527A pdb=" N GLN A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 800 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN A 806 " --> pdb=" O HIS A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 830 removed outlier: 4.076A pdb=" N GLN A 816 " --> pdb=" O GLN A 812 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 817 " --> pdb=" O THR A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 861 removed outlier: 3.975A pdb=" N CYS A 857 " --> pdb=" O ARG A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 removed outlier: 3.714A pdb=" N LEU A 866 " --> pdb=" O MET A 862 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N MET A 877 " --> pdb=" O HIS A 873 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N HIS A 878 " --> pdb=" O GLN A 874 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU A 879 " --> pdb=" O CYS A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 897 removed outlier: 3.769A pdb=" N MET A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 921 removed outlier: 3.526A pdb=" N ALA A 913 " --> pdb=" O ASN A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 934 removed outlier: 3.906A pdb=" N VAL A 932 " --> pdb=" O ASP A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 950 removed outlier: 3.647A pdb=" N ILE A 946 " --> pdb=" O ILE A 942 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN A 947 " --> pdb=" O ASN A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 988 removed outlier: 4.009A pdb=" N PHE A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 971 " --> pdb=" O ARG A 967 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA A 974 " --> pdb=" O PHE A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1005 removed outlier: 3.617A pdb=" N GLN A1005 " --> pdb=" O THR A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1014 Processing helix chain 'A' and resid 1015 through 1016 No H-bonds generated for 'chain 'A' and resid 1015 through 1016' Processing helix chain 'A' and resid 1017 through 1021 Processing helix chain 'A' and resid 1027 through 1031 removed outlier: 3.734A pdb=" N LEU A1030 " --> pdb=" O GLY A1027 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS A1031 " --> pdb=" O PRO A1028 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1027 through 1031' Processing helix chain 'A' and resid 1032 through 1055 Processing helix chain 'A' and resid 1056 through 1069 removed outlier: 3.997A pdb=" N ALA A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1079 Processing helix chain 'A' and resid 1084 through 1090 removed outlier: 4.094A pdb=" N GLU A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1099 removed outlier: 3.548A pdb=" N LEU A1097 " --> pdb=" O ASP A1094 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU A1099 " --> pdb=" O GLN A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1115 removed outlier: 3.608A pdb=" N GLN A1105 " --> pdb=" O SER A1101 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A1109 " --> pdb=" O GLN A1105 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A1110 " --> pdb=" O LYS A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 removed outlier: 3.978A pdb=" N LEU A1124 " --> pdb=" O HIS A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1166 removed outlier: 3.520A pdb=" N GLU A1147 " --> pdb=" O ASN A1143 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1182 removed outlier: 3.779A pdb=" N LEU A1176 " --> pdb=" O GLY A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1194 Processing helix chain 'A' and resid 1203 through 1208 removed outlier: 4.184A pdb=" N LYS A1207 " --> pdb=" O ASN A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1232 Processing helix chain 'A' and resid 1233 through 1245 removed outlier: 4.529A pdb=" N VAL A1237 " --> pdb=" O ASP A1233 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS A1238 " --> pdb=" O LEU A1234 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A1243 " --> pdb=" O THR A1239 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS A1244 " --> pdb=" O PHE A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1255 removed outlier: 3.855A pdb=" N PHE A1252 " --> pdb=" O ARG A1248 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A1253 " --> pdb=" O LEU A1249 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A1254 " --> pdb=" O LYS A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1271 removed outlier: 3.698A pdb=" N THR A1271 " --> pdb=" O GLN A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1332 removed outlier: 3.766A pdb=" N GLU A1330 " --> pdb=" O MET A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1348 removed outlier: 3.681A pdb=" N ALA A1338 " --> pdb=" O PHE A1334 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A1347 " --> pdb=" O PHE A1343 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A1348 " --> pdb=" O ILE A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1356 removed outlier: 3.518A pdb=" N ARG A1356 " --> pdb=" O LYS A1353 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 524 Processing helix chain 'B' and resid 560 through 577 removed outlier: 3.806A pdb=" N GLU B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 575 " --> pdb=" O ALA B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 601 Processing helix chain 'B' and resid 607 through 616 removed outlier: 3.645A pdb=" N LEU B 611 " --> pdb=" O ARG B 607 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 612 " --> pdb=" O VAL B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 630 removed outlier: 3.622A pdb=" N ILE B 623 " --> pdb=" O SER B 619 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU B 624 " --> pdb=" O PRO B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 685 removed outlier: 4.379A pdb=" N GLN B 674 " --> pdb=" O ARG B 670 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 708 removed outlier: 4.155A pdb=" N ARG B 696 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET B 697 " --> pdb=" O SER B 693 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU B 701 " --> pdb=" O MET B 697 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER B 702 " --> pdb=" O TYR B 698 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 708 " --> pdb=" O LYS B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 721 removed outlier: 4.031A pdb=" N VAL B 715 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU B 718 " --> pdb=" O SER B 714 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN B 719 " --> pdb=" O VAL B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 749 removed outlier: 3.575A pdb=" N LEU B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU B 748 " --> pdb=" O GLU B 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 521 removed outlier: 3.587A pdb=" N TYR C 519 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET C 520 " --> pdb=" O LEU C 516 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN C 521 " --> pdb=" O HIS C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 577 removed outlier: 3.553A pdb=" N LYS C 565 " --> pdb=" O LYS C 561 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN C 566 " --> pdb=" O LYS C 562 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG C 570 " --> pdb=" O ASN C 566 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR C 572 " --> pdb=" O ALA C 568 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU C 573 " --> pdb=" O ALA C 569 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU C 574 " --> pdb=" O ARG C 570 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE C 575 " --> pdb=" O ALA C 571 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 576 " --> pdb=" O THR C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 749 removed outlier: 3.794A pdb=" N LEU C 732 " --> pdb=" O ASN C 728 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 413 through 415 removed outlier: 3.665A pdb=" N ARG A 684 " --> pdb=" O GLY A 603 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY A 603 " --> pdb=" O ARG A 684 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 686 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N PHE A 601 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N PHE A 688 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 9.656A pdb=" N TYR A 599 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 608 " --> pdb=" O PHE A 572 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 413 through 415 removed outlier: 3.665A pdb=" N ARG A 684 " --> pdb=" O GLY A 603 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY A 603 " --> pdb=" O ARG A 684 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 686 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N PHE A 601 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N PHE A 688 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 9.656A pdb=" N TYR A 599 " --> pdb=" O PHE A 688 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA4, first strand: chain 'A' and resid 576 through 578 removed outlier: 4.186A pdb=" N CYS A 618 " --> pdb=" O ILE A 629 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 751 through 753 removed outlier: 4.539A pdb=" N ILE A 741 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR A 850 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 771 through 777 Processing sheet with id=AA7, first strand: chain 'A' and resid 1283 through 1290 removed outlier: 3.574A pdb=" N ALA A1301 " --> pdb=" O LYS A1285 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR A1299 " --> pdb=" O LEU A1287 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR A1289 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR A1297 " --> pdb=" O THR A1289 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR A1298 " --> pdb=" O LYS A1313 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS A1313 " --> pdb=" O TYR A1298 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A1300 " --> pdb=" O CYS A1311 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N CYS A1311 " --> pdb=" O VAL A1300 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A1302 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 495 through 496 Processing sheet with id=AA9, first strand: chain 'B' and resid 530 through 534 removed outlier: 7.255A pdb=" N ALA B 544 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER B 555 " --> pdb=" O ALA B 544 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL B 546 " --> pdb=" O TYR B 553 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR B 553 " --> pdb=" O VAL B 546 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 639 through 644 removed outlier: 3.613A pdb=" N SER B 651 " --> pdb=" O CYS B 666 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 655 " --> pdb=" O VAL B 662 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3662 1.34 - 1.46: 3270 1.46 - 1.58: 5471 1.58 - 1.71: 190 1.71 - 1.83: 101 Bond restraints: 12694 Sorted by residual: bond pdb=" C PHE A1166 " pdb=" N PRO A1167 " ideal model delta sigma weight residual 1.331 1.319 0.012 7.90e-03 1.60e+04 2.35e+00 bond pdb=" C3' A E 73 " pdb=" O3' A E 73 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.29e+00 bond pdb=" CB ILE A1153 " pdb=" CG2 ILE A1153 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.07e+00 bond pdb=" CB TRP A 794 " pdb=" CG TRP A 794 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.04e+00 bond pdb=" CG MET A 935 " pdb=" SD MET A 935 " ideal model delta sigma weight residual 1.803 1.828 -0.025 2.50e-02 1.60e+03 1.01e+00 ... (remaining 12689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 17171 1.66 - 3.32: 365 3.32 - 4.98: 48 4.98 - 6.64: 10 6.64 - 8.30: 7 Bond angle restraints: 17601 Sorted by residual: angle pdb=" C3' A E 73 " pdb=" O3' A E 73 " pdb=" P A E 74 " ideal model delta sigma weight residual 120.20 124.92 -4.72 1.50e+00 4.44e-01 9.90e+00 angle pdb=" CA MET B 634 " pdb=" CB MET B 634 " pdb=" CG MET B 634 " ideal model delta sigma weight residual 114.10 120.06 -5.96 2.00e+00 2.50e-01 8.87e+00 angle pdb=" N ARG A1208 " pdb=" CA ARG A1208 " pdb=" C ARG A1208 " ideal model delta sigma weight residual 108.13 110.74 -2.61 9.00e-01 1.23e+00 8.38e+00 angle pdb=" N GLY A 692 " pdb=" CA GLY A 692 " pdb=" C GLY A 692 " ideal model delta sigma weight residual 114.48 111.15 3.33 1.19e+00 7.06e-01 7.83e+00 angle pdb=" CB MET B 634 " pdb=" CG MET B 634 " pdb=" SD MET B 634 " ideal model delta sigma weight residual 112.70 121.00 -8.30 3.00e+00 1.11e-01 7.65e+00 ... (remaining 17596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 7391 35.22 - 70.43: 403 70.43 - 105.65: 35 105.65 - 140.86: 1 140.86 - 176.08: 2 Dihedral angle restraints: 7832 sinusoidal: 4151 harmonic: 3681 Sorted by residual: dihedral pdb=" O4' U E 72 " pdb=" C1' U E 72 " pdb=" N1 U E 72 " pdb=" C2 U E 72 " ideal model delta sinusoidal sigma weight residual -128.00 48.08 -176.08 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U E 47 " pdb=" C1' U E 47 " pdb=" N1 U E 47 " pdb=" C2 U E 47 " ideal model delta sinusoidal sigma weight residual -128.00 -61.37 -66.63 1 1.70e+01 3.46e-03 2.00e+01 dihedral pdb=" C4' A E 73 " pdb=" C3' A E 73 " pdb=" O3' A E 73 " pdb=" P A E 74 " ideal model delta sinusoidal sigma weight residual -110.00 53.35 -163.35 1 3.50e+01 8.16e-04 1.53e+01 ... (remaining 7829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1378 0.032 - 0.064: 424 0.064 - 0.095: 141 0.095 - 0.127: 48 0.127 - 0.159: 9 Chirality restraints: 2000 Sorted by residual: chirality pdb=" C3' A E 73 " pdb=" C4' A E 73 " pdb=" O3' A E 73 " pdb=" C2' A E 73 " both_signs ideal model delta sigma weight residual False -2.74 -2.59 -0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA SER A 579 " pdb=" N SER A 579 " pdb=" C SER A 579 " pdb=" CB SER A 579 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ILE A 741 " pdb=" N ILE A 741 " pdb=" C ILE A 741 " pdb=" CB ILE A 741 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 1997 not shown) Planarity restraints: 1918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A1027 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A1028 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A1028 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1028 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 725 " -0.018 2.00e-02 2.50e+03 1.33e-02 4.45e+00 pdb=" CG TRP A 725 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 725 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 725 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 725 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 725 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 725 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 725 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 725 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 725 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A1246 " 0.031 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO A1247 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A1247 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1247 " 0.026 5.00e-02 4.00e+02 ... (remaining 1915 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1234 2.74 - 3.28: 11979 3.28 - 3.82: 20338 3.82 - 4.36: 23070 4.36 - 4.90: 37377 Nonbonded interactions: 93998 Sorted by model distance: nonbonded pdb=" NZ LYS C 561 " pdb=" OP1 A E 33 " model vdw 2.196 3.120 nonbonded pdb=" O2' G E 68 " pdb=" O4' A E 69 " model vdw 2.201 3.040 nonbonded pdb=" NE2 HIS C 517 " pdb=" O2' A E 77 " model vdw 2.208 3.120 nonbonded pdb=" OH TYR A 885 " pdb=" OE1 GLU A1054 " model vdw 2.220 3.040 nonbonded pdb=" O PHE B 542 " pdb=" OG1 THR B 557 " model vdw 2.227 3.040 ... (remaining 93993 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 35.140 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 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 : 0.004 0.046 12702 Z= 0.205 Angle : 0.616 8.300 17605 Z= 0.322 Chirality : 0.038 0.159 2000 Planarity : 0.004 0.053 1918 Dihedral : 19.266 176.079 5446 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.09 % Allowed : 22.45 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.24), residues: 1244 helix: 1.67 (0.23), residues: 536 sheet: -0.58 (0.55), residues: 98 loop : -1.35 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 725 HIS 0.006 0.001 HIS C 517 PHE 0.025 0.001 PHE C 532 TYR 0.013 0.001 TYR A1199 ARG 0.011 0.001 ARG B 696 Details of bonding type rmsd hydrogen bonds : bond 0.20577 ( 515) hydrogen bonds : angle 6.14154 ( 1421) metal coordination : bond 0.00925 ( 8) metal coordination : angle 0.58789 ( 4) covalent geometry : bond 0.00448 (12694) covalent geometry : angle 0.61623 (17601) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 1.365 Fit side-chains REVERT: C 570 ARG cc_start: 0.8342 (mtm110) cc_final: 0.7214 (ttp80) outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.2403 time to fit residues: 17.9866 Evaluate side-chains 47 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 897 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 ASN B 649 GLN ** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 678 GLN B 730 HIS C 521 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.056933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.039319 restraints weight = 82273.479| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.26 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12702 Z= 0.217 Angle : 0.599 6.448 17605 Z= 0.306 Chirality : 0.038 0.161 2000 Planarity : 0.004 0.048 1918 Dihedral : 18.791 176.528 2842 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.22 % Allowed : 20.39 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.24), residues: 1244 helix: 1.55 (0.22), residues: 567 sheet: -0.55 (0.54), residues: 101 loop : -1.33 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 725 HIS 0.004 0.001 HIS B 685 PHE 0.013 0.001 PHE B 598 TYR 0.014 0.001 TYR B 698 ARG 0.003 0.000 ARG B 741 Details of bonding type rmsd hydrogen bonds : bond 0.06708 ( 515) hydrogen bonds : angle 4.52282 ( 1421) metal coordination : bond 0.01009 ( 8) metal coordination : angle 1.33714 ( 4) covalent geometry : bond 0.00485 (12694) covalent geometry : angle 0.59871 (17601) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 46 time to evaluate : 1.201 Fit side-chains outliers start: 36 outliers final: 12 residues processed: 78 average time/residue: 0.1962 time to fit residues: 24.7191 Evaluate side-chains 58 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain C residue 545 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 25 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 113 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 129 optimal weight: 50.0000 chunk 21 optimal weight: 0.1980 chunk 74 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 HIS ** 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 = 0.3765 r_free = 0.3765 target = 0.056912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.038827 restraints weight = 82932.308| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 4.56 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12702 Z= 0.167 Angle : 0.548 6.680 17605 Z= 0.278 Chirality : 0.037 0.163 2000 Planarity : 0.004 0.048 1918 Dihedral : 18.704 176.890 2839 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.59 % Allowed : 21.11 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1244 helix: 1.63 (0.22), residues: 574 sheet: -0.66 (0.55), residues: 99 loop : -1.30 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 725 HIS 0.005 0.001 HIS C 517 PHE 0.009 0.001 PHE A1148 TYR 0.010 0.001 TYR B 698 ARG 0.005 0.000 ARG C 570 Details of bonding type rmsd hydrogen bonds : bond 0.05619 ( 515) hydrogen bonds : angle 4.07760 ( 1421) metal coordination : bond 0.00633 ( 8) metal coordination : angle 1.29648 ( 4) covalent geometry : bond 0.00375 (12694) covalent geometry : angle 0.54773 (17601) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 46 time to evaluate : 1.313 Fit side-chains REVERT: A 425 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7966 (t0) REVERT: B 697 MET cc_start: 0.8846 (mpp) cc_final: 0.8093 (ptm) REVERT: B 712 ASP cc_start: 0.9347 (t0) cc_final: 0.8897 (p0) outliers start: 29 outliers final: 14 residues processed: 73 average time/residue: 0.2160 time to fit residues: 24.9320 Evaluate side-chains 61 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 576 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 45 optimal weight: 4.9990 chunk 101 optimal weight: 0.4980 chunk 94 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 76 optimal weight: 0.0020 chunk 95 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 118 optimal weight: 0.0870 chunk 11 optimal weight: 0.0970 chunk 47 optimal weight: 6.9990 chunk 92 optimal weight: 30.0000 overall best weight: 0.7366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN A 763 ASN A1294 HIS ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.057583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.039930 restraints weight = 81944.492| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.36 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12702 Z= 0.095 Angle : 0.494 6.658 17605 Z= 0.250 Chirality : 0.035 0.165 2000 Planarity : 0.004 0.044 1918 Dihedral : 18.539 176.103 2839 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.88 % Allowed : 22.00 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1244 helix: 1.79 (0.22), residues: 576 sheet: -0.48 (0.53), residues: 99 loop : -1.26 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 725 HIS 0.003 0.001 HIS B 600 PHE 0.009 0.001 PHE B 598 TYR 0.008 0.001 TYR B 698 ARG 0.004 0.000 ARG C 570 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 515) hydrogen bonds : angle 3.71076 ( 1421) metal coordination : bond 0.00521 ( 8) metal coordination : angle 1.40022 ( 4) covalent geometry : bond 0.00203 (12694) covalent geometry : angle 0.49408 (17601) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 1.191 Fit side-chains REVERT: A 949 MET cc_start: 0.8974 (mmm) cc_final: 0.8526 (mtm) REVERT: B 639 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7110 (mm) REVERT: B 712 ASP cc_start: 0.9354 (t0) cc_final: 0.8922 (p0) outliers start: 21 outliers final: 9 residues processed: 65 average time/residue: 0.2108 time to fit residues: 22.1708 Evaluate side-chains 56 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 576 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 58 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 91 optimal weight: 40.0000 chunk 66 optimal weight: 0.0970 chunk 114 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 933 HIS ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.056341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.039699 restraints weight = 82728.111| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 4.69 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12702 Z= 0.224 Angle : 0.575 6.534 17605 Z= 0.291 Chirality : 0.038 0.164 2000 Planarity : 0.004 0.051 1918 Dihedral : 18.576 176.090 2839 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.77 % Allowed : 21.74 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1244 helix: 1.72 (0.22), residues: 575 sheet: -0.44 (0.53), residues: 101 loop : -1.34 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 725 HIS 0.004 0.001 HIS A 630 PHE 0.009 0.001 PHE A1163 TYR 0.012 0.001 TYR A 784 ARG 0.002 0.000 ARG A 923 Details of bonding type rmsd hydrogen bonds : bond 0.06162 ( 515) hydrogen bonds : angle 3.99202 ( 1421) metal coordination : bond 0.01041 ( 8) metal coordination : angle 1.31683 ( 4) covalent geometry : bond 0.00504 (12694) covalent geometry : angle 0.57445 (17601) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 46 time to evaluate : 1.179 Fit side-chains REVERT: A 425 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.8043 (t0) REVERT: A 602 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7551 (pp20) REVERT: A 939 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8941 (ttmm) REVERT: A 1087 GLN cc_start: 0.9510 (OUTLIER) cc_final: 0.9283 (pt0) REVERT: B 639 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8083 (mm) REVERT: B 697 MET cc_start: 0.8970 (mpp) cc_final: 0.7947 (ptm) REVERT: B 712 ASP cc_start: 0.9323 (t0) cc_final: 0.8831 (p0) outliers start: 31 outliers final: 19 residues processed: 75 average time/residue: 0.2277 time to fit residues: 27.9580 Evaluate side-chains 70 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 939 LYS Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 735 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 118 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 116 optimal weight: 30.0000 chunk 129 optimal weight: 50.0000 chunk 44 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 HIS ** 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 = 0.3752 r_free = 0.3752 target = 0.056359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.039848 restraints weight = 83005.833| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 4.48 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12702 Z= 0.194 Angle : 0.548 6.241 17605 Z= 0.276 Chirality : 0.037 0.166 2000 Planarity : 0.004 0.049 1918 Dihedral : 18.614 175.025 2839 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.59 % Allowed : 21.82 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.24), residues: 1244 helix: 1.66 (0.22), residues: 575 sheet: -0.34 (0.52), residues: 106 loop : -1.36 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 725 HIS 0.004 0.001 HIS A 630 PHE 0.009 0.001 PHE A1148 TYR 0.010 0.001 TYR B 698 ARG 0.002 0.000 ARG A 923 Details of bonding type rmsd hydrogen bonds : bond 0.05623 ( 515) hydrogen bonds : angle 3.85811 ( 1421) metal coordination : bond 0.00911 ( 8) metal coordination : angle 1.27725 ( 4) covalent geometry : bond 0.00440 (12694) covalent geometry : angle 0.54750 (17601) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 47 time to evaluate : 1.233 Fit side-chains REVERT: A 425 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7997 (t0) REVERT: A 602 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7456 (pp20) REVERT: A 939 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.8923 (ttmm) REVERT: B 600 HIS cc_start: 0.8755 (t70) cc_final: 0.8457 (m170) REVERT: B 639 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8160 (mm) REVERT: B 697 MET cc_start: 0.9013 (mpp) cc_final: 0.7975 (ptm) REVERT: B 712 ASP cc_start: 0.9267 (t0) cc_final: 0.8737 (p0) REVERT: C 570 ARG cc_start: 0.8940 (mpp80) cc_final: 0.8646 (mmm160) outliers start: 29 outliers final: 18 residues processed: 75 average time/residue: 0.2079 time to fit residues: 25.2020 Evaluate side-chains 69 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 939 LYS Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 576 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 112 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 HIS ** 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 = 0.3735 r_free = 0.3735 target = 0.055708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.038936 restraints weight = 83341.086| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.64 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12702 Z= 0.273 Angle : 0.616 7.897 17605 Z= 0.309 Chirality : 0.039 0.164 2000 Planarity : 0.004 0.053 1918 Dihedral : 18.708 172.983 2839 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.95 % Allowed : 21.38 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.24), residues: 1244 helix: 1.51 (0.22), residues: 575 sheet: -0.46 (0.51), residues: 104 loop : -1.41 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 725 HIS 0.005 0.001 HIS A 630 PHE 0.012 0.001 PHE A1163 TYR 0.013 0.002 TYR A 784 ARG 0.003 0.000 ARG A 961 Details of bonding type rmsd hydrogen bonds : bond 0.06751 ( 515) hydrogen bonds : angle 4.12893 ( 1421) metal coordination : bond 0.01197 ( 8) metal coordination : angle 1.33928 ( 4) covalent geometry : bond 0.00619 (12694) covalent geometry : angle 0.61556 (17601) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 47 time to evaluate : 1.260 Fit side-chains REVERT: A 425 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7951 (t0) REVERT: A 602 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7548 (pp20) REVERT: A 939 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8948 (ttmm) REVERT: A 1087 GLN cc_start: 0.9525 (OUTLIER) cc_final: 0.9280 (pt0) REVERT: B 600 HIS cc_start: 0.8858 (t70) cc_final: 0.8547 (m170) REVERT: B 639 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8241 (mm) REVERT: B 697 MET cc_start: 0.9042 (mpp) cc_final: 0.8118 (ptm) REVERT: B 712 ASP cc_start: 0.9274 (t0) cc_final: 0.8766 (p0) REVERT: C 570 ARG cc_start: 0.8963 (mpp80) cc_final: 0.8687 (mmm160) outliers start: 33 outliers final: 23 residues processed: 79 average time/residue: 0.2377 time to fit residues: 30.2765 Evaluate side-chains 75 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 47 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 939 LYS Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 735 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 53 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 120 optimal weight: 40.0000 chunk 12 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 HIS ** 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 = 0.3771 r_free = 0.3771 target = 0.056922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.040363 restraints weight = 84813.361| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 4.83 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12702 Z= 0.106 Angle : 0.508 6.935 17605 Z= 0.256 Chirality : 0.036 0.167 2000 Planarity : 0.004 0.048 1918 Dihedral : 18.578 172.248 2839 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.79 % Allowed : 22.45 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.24), residues: 1244 helix: 1.77 (0.22), residues: 581 sheet: -0.37 (0.52), residues: 104 loop : -1.40 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 725 HIS 0.003 0.001 HIS B 600 PHE 0.010 0.001 PHE A1148 TYR 0.009 0.001 TYR A1229 ARG 0.006 0.000 ARG A 923 Details of bonding type rmsd hydrogen bonds : bond 0.04719 ( 515) hydrogen bonds : angle 3.67771 ( 1421) metal coordination : bond 0.00559 ( 8) metal coordination : angle 1.43459 ( 4) covalent geometry : bond 0.00230 (12694) covalent geometry : angle 0.50769 (17601) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 1.622 Fit side-chains REVERT: A 425 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7985 (t0) REVERT: A 602 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7404 (pp20) REVERT: B 600 HIS cc_start: 0.8828 (t70) cc_final: 0.8525 (m170) REVERT: B 639 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8027 (mm) REVERT: B 697 MET cc_start: 0.9015 (mpp) cc_final: 0.8090 (ptm) REVERT: B 712 ASP cc_start: 0.9271 (t0) cc_final: 0.8766 (p0) outliers start: 20 outliers final: 13 residues processed: 67 average time/residue: 0.2682 time to fit residues: 28.3319 Evaluate side-chains 63 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 576 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 78 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 101 optimal weight: 0.0070 chunk 95 optimal weight: 0.2980 chunk 86 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.0604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 HIS ** 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 = 0.3761 r_free = 0.3761 target = 0.056680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.039140 restraints weight = 84798.315| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 4.20 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12702 Z= 0.148 Angle : 0.528 7.161 17605 Z= 0.264 Chirality : 0.036 0.167 2000 Planarity : 0.004 0.050 1918 Dihedral : 18.525 172.626 2839 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.97 % Allowed : 22.36 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1244 helix: 1.82 (0.22), residues: 582 sheet: -0.21 (0.52), residues: 106 loop : -1.42 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 725 HIS 0.004 0.001 HIS B 600 PHE 0.009 0.001 PHE A1148 TYR 0.010 0.001 TYR B 698 ARG 0.004 0.000 ARG C 570 Details of bonding type rmsd hydrogen bonds : bond 0.05210 ( 515) hydrogen bonds : angle 3.70181 ( 1421) metal coordination : bond 0.00538 ( 8) metal coordination : angle 1.31806 ( 4) covalent geometry : bond 0.00336 (12694) covalent geometry : angle 0.52754 (17601) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 1.140 Fit side-chains REVERT: A 425 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7711 (t0) REVERT: A 602 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7525 (pp20) REVERT: A 949 MET cc_start: 0.8981 (mmm) cc_final: 0.8601 (mtm) REVERT: A 1087 GLN cc_start: 0.9478 (OUTLIER) cc_final: 0.9272 (pt0) REVERT: B 600 HIS cc_start: 0.8914 (t70) cc_final: 0.8581 (m170) REVERT: B 639 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7633 (mm) REVERT: B 697 MET cc_start: 0.8925 (mpp) cc_final: 0.8092 (ptm) REVERT: B 712 ASP cc_start: 0.9333 (t0) cc_final: 0.8858 (p0) outliers start: 22 outliers final: 18 residues processed: 69 average time/residue: 0.2010 time to fit residues: 22.4583 Evaluate side-chains 70 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 735 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 25 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.056561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.040087 restraints weight = 84244.533| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 4.37 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12702 Z= 0.165 Angle : 0.540 7.915 17605 Z= 0.269 Chirality : 0.037 0.166 2000 Planarity : 0.004 0.050 1918 Dihedral : 18.516 172.516 2839 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.97 % Allowed : 22.63 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1244 helix: 1.81 (0.22), residues: 581 sheet: -0.20 (0.52), residues: 106 loop : -1.41 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 725 HIS 0.004 0.001 HIS B 600 PHE 0.009 0.001 PHE C 542 TYR 0.015 0.001 TYR A 784 ARG 0.008 0.000 ARG C 570 Details of bonding type rmsd hydrogen bonds : bond 0.05333 ( 515) hydrogen bonds : angle 3.73143 ( 1421) metal coordination : bond 0.00671 ( 8) metal coordination : angle 1.39053 ( 4) covalent geometry : bond 0.00374 (12694) covalent geometry : angle 0.53959 (17601) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 1.311 Fit side-chains REVERT: A 425 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.7952 (t0) REVERT: A 602 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7520 (pp20) REVERT: A 949 MET cc_start: 0.8950 (mmm) cc_final: 0.8598 (mtm) REVERT: A 1087 GLN cc_start: 0.9500 (OUTLIER) cc_final: 0.9285 (pt0) REVERT: B 600 HIS cc_start: 0.8838 (t70) cc_final: 0.8552 (m170) REVERT: B 639 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8196 (mm) REVERT: B 697 MET cc_start: 0.9034 (mpp) cc_final: 0.8113 (ptm) REVERT: B 712 ASP cc_start: 0.9257 (t0) cc_final: 0.8733 (p0) outliers start: 22 outliers final: 17 residues processed: 70 average time/residue: 0.1990 time to fit residues: 22.6553 Evaluate side-chains 70 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 735 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 69 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 51 optimal weight: 0.0070 chunk 58 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.057205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.039790 restraints weight = 84771.771| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 4.47 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12702 Z= 0.102 Angle : 0.512 9.537 17605 Z= 0.253 Chirality : 0.035 0.167 2000 Planarity : 0.004 0.048 1918 Dihedral : 18.428 172.570 2839 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.52 % Allowed : 22.90 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1244 helix: 1.90 (0.22), residues: 580 sheet: -0.21 (0.52), residues: 104 loop : -1.34 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 725 HIS 0.003 0.001 HIS B 600 PHE 0.010 0.001 PHE A1148 TYR 0.008 0.001 TYR B 698 ARG 0.008 0.000 ARG C 570 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 515) hydrogen bonds : angle 3.50861 ( 1421) metal coordination : bond 0.00488 ( 8) metal coordination : angle 1.53732 ( 4) covalent geometry : bond 0.00225 (12694) covalent geometry : angle 0.51191 (17601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5779.20 seconds wall clock time: 101 minutes 50.63 seconds (6110.63 seconds total)