Starting phenix.real_space_refine on Wed May 14 21:37:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asp_43822/05_2025/9asp_43822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asp_43822/05_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_43822/05_2025/9asp_43822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asp_43822/05_2025/9asp_43822.map" model { file = "/net/cci-nas-00/data/ceres_data/9asp_43822/05_2025/9asp_43822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asp_43822/05_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-5687/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: 7.47, 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: 3.00 Conformation dependent library (CDL) restraints added in 1.5 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: 3.98 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: 4.88 Time building geometry restraints manager: 3.55 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: 1.850 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 34.980 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.480 ------------------------------------------------------------------------------- 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 : 1.239 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: 0.2266 time to fit residues: 16.6763 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 : 1.238 ------------------------------------------------------------------------------- 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 = 61)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.039278 restraints weight = 82273.372| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 4.26 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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 4.52283 ( 1421) metal coordination : bond 0.01009 ( 8) metal coordination : angle 1.33715 ( 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 : 1.275 Fit side-chains outliers start: 36 outliers final: 12 residues processed: 78 average time/residue: 0.1929 time to fit residues: 24.1586 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 : 1.212 ------------------------------------------------------------------------------- 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: 10.0000 chunk 61 optimal weight: 5.9990 chunk 30 optimal weight: 0.0770 chunk 113 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 129 optimal weight: 50.0000 chunk 21 optimal weight: 0.2980 chunk 74 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 overall best weight: 1.8342 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.057139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.040287 restraints weight = 83435.252| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 4.46 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1341 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= 0.140 Angle : 0.532 6.304 17605 Z= 0.270 Chirality : 0.037 0.163 2000 Planarity : 0.004 0.047 1918 Dihedral : 18.681 176.863 2839 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.24 % Allowed : 21.11 % Favored : 76.65 % 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: 0.27 (0.24), residues: 1244 helix: 1.70 (0.22), residues: 571 sheet: -0.64 (0.55), residues: 99 loop : -1.28 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 725 HIS 0.005 0.001 HIS C 517 PHE 0.008 0.001 PHE B 598 TYR 0.010 0.001 TYR B 698 ARG 0.004 0.000 ARG C 570 Details of bonding type rmsd hydrogen bonds : bond 0.05379 ( 515) hydrogen bonds : angle 4.05116 ( 1421) metal coordination : bond 0.00454 ( 8) metal coordination : angle 1.18859 ( 4) covalent geometry : bond 0.00310 (12694) covalent geometry : angle 0.53145 (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 71 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 46 time to evaluate : 1.236 Fit side-chains REVERT: A 425 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7977 (t0) REVERT: B 600 HIS cc_start: 0.8629 (t70) cc_final: 0.8377 (m170) REVERT: B 712 ASP cc_start: 0.9295 (t0) cc_final: 0.8808 (p0) outliers start: 25 outliers final: 12 residues processed: 69 average time/residue: 0.2068 time to fit residues: 22.4968 Evaluate side-chains 59 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 101 optimal weight: 6.9990 chunk 94 optimal weight: 0.0870 chunk 131 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 95 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 92 optimal weight: 40.0000 overall best weight: 1.8962 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.057152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.040638 restraints weight = 82799.784| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 4.65 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1684 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= 0.141 Angle : 0.516 6.230 17605 Z= 0.261 Chirality : 0.036 0.164 2000 Planarity : 0.004 0.047 1918 Dihedral : 18.562 176.021 2839 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.68 % Allowed : 21.29 % Favored : 76.03 % 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: 0.31 (0.24), residues: 1244 helix: 1.74 (0.22), residues: 574 sheet: -0.57 (0.53), residues: 99 loop : -1.31 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 725 HIS 0.003 0.001 HIS A 630 PHE 0.008 0.001 PHE B 598 TYR 0.010 0.001 TYR B 698 ARG 0.005 0.000 ARG C 570 Details of bonding type rmsd hydrogen bonds : bond 0.05147 ( 515) hydrogen bonds : angle 3.83292 ( 1421) metal coordination : bond 0.00527 ( 8) metal coordination : angle 1.36379 ( 4) covalent geometry : bond 0.00317 (12694) covalent geometry : angle 0.51549 (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 77 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 47 time to evaluate : 1.264 Fit side-chains REVERT: A 425 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8085 (t0) REVERT: A 602 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7531 (pp20) REVERT: B 639 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8077 (mm) REVERT: B 697 MET cc_start: 0.8959 (mpp) cc_final: 0.7949 (ptm) REVERT: B 712 ASP cc_start: 0.9312 (t0) cc_final: 0.8801 (p0) outliers start: 30 outliers final: 17 residues processed: 76 average time/residue: 0.2182 time to fit residues: 26.4466 Evaluate side-chains 65 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 725 TRP 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 1038 HIS 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 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 526 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: 0.0870 chunk 117 optimal weight: 30.0000 chunk 33 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 91 optimal weight: 40.0000 chunk 66 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN A1294 HIS ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.057635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.039833 restraints weight = 83715.992| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 4.55 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1990 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= 0.095 Angle : 0.481 6.176 17605 Z= 0.243 Chirality : 0.035 0.167 2000 Planarity : 0.003 0.045 1918 Dihedral : 18.464 176.085 2839 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.97 % Allowed : 22.18 % Favored : 75.85 % 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: 0.47 (0.24), residues: 1244 helix: 1.87 (0.22), residues: 580 sheet: -0.42 (0.56), residues: 89 loop : -1.26 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 725 HIS 0.003 0.001 HIS B 600 PHE 0.009 0.001 PHE A 970 TYR 0.008 0.001 TYR A1199 ARG 0.003 0.000 ARG C 570 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 515) hydrogen bonds : angle 3.60802 ( 1421) metal coordination : bond 0.00490 ( 8) metal coordination : angle 1.40828 ( 4) covalent geometry : bond 0.00205 (12694) covalent geometry : angle 0.48107 (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 68 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 1.461 Fit side-chains revert: symmetry clash REVERT: A 425 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.7975 (t0) REVERT: B 639 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7414 (mm) REVERT: B 697 MET cc_start: 0.8856 (mpp) cc_final: 0.8057 (ptm) REVERT: B 712 ASP cc_start: 0.9333 (t0) cc_final: 0.8807 (p0) REVERT: C 570 ARG cc_start: 0.8751 (mtm110) cc_final: 0.8348 (mmm160) outliers start: 22 outliers final: 12 residues processed: 66 average time/residue: 0.2133 time to fit residues: 22.6991 Evaluate side-chains 60 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1038 HIS 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 642 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 118 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 116 optimal weight: 30.0000 chunk 129 optimal weight: 50.0000 chunk 44 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** ** C 728 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 = 0.3735 r_free = 0.3735 target = 0.055849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.039023 restraints weight = 83454.168| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 4.73 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 12702 Z= 0.320 Angle : 0.646 7.243 17605 Z= 0.325 Chirality : 0.040 0.163 2000 Planarity : 0.004 0.055 1918 Dihedral : 18.617 175.419 2839 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.68 % Allowed : 21.38 % Favored : 75.94 % 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: 0.15 (0.24), residues: 1244 helix: 1.55 (0.22), residues: 577 sheet: -0.37 (0.52), residues: 104 loop : -1.40 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 725 HIS 0.006 0.001 HIS A 630 PHE 0.014 0.002 PHE A1163 TYR 0.017 0.002 TYR A 784 ARG 0.003 0.000 ARG C 570 Details of bonding type rmsd hydrogen bonds : bond 0.07061 ( 515) hydrogen bonds : angle 4.17785 ( 1421) metal coordination : bond 0.01533 ( 8) metal coordination : angle 1.56062 ( 4) covalent geometry : bond 0.00723 (12694) covalent geometry : angle 0.64540 (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 77 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 47 time to evaluate : 1.254 Fit side-chains REVERT: A 425 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.8057 (t0) REVERT: A 602 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7588 (pp20) REVERT: A 699 MET cc_start: 0.8172 (mmm) cc_final: 0.7673 (tpp) REVERT: A 939 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8964 (ttmm) REVERT: A 1087 GLN cc_start: 0.9517 (OUTLIER) cc_final: 0.9269 (pt0) REVERT: B 600 HIS cc_start: 0.8812 (t70) cc_final: 0.8477 (m170) REVERT: B 639 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8083 (mm) REVERT: B 697 MET cc_start: 0.9051 (mpp) cc_final: 0.8106 (ptm) REVERT: B 712 ASP cc_start: 0.9289 (t0) cc_final: 0.8781 (p0) outliers start: 30 outliers final: 21 residues processed: 76 average time/residue: 0.2165 time to fit residues: 26.0704 Evaluate side-chains 72 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 46 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 704 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 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 642 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 112 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 ** 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 = 0.3769 r_free = 0.3769 target = 0.056921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.040339 restraints weight = 84069.493| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 4.65 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12702 Z= 0.130 Angle : 0.513 6.553 17605 Z= 0.258 Chirality : 0.036 0.166 2000 Planarity : 0.004 0.089 1918 Dihedral : 18.574 173.995 2839 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.70 % Allowed : 22.72 % 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: 0.36 (0.24), residues: 1244 helix: 1.81 (0.22), residues: 581 sheet: -0.28 (0.52), residues: 106 loop : -1.42 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 725 HIS 0.004 0.001 HIS C 517 PHE 0.009 0.001 PHE A1148 TYR 0.010 0.001 TYR A1229 ARG 0.002 0.000 ARG A 923 Details of bonding type rmsd hydrogen bonds : bond 0.05044 ( 515) hydrogen bonds : angle 3.74500 ( 1421) metal coordination : bond 0.00581 ( 8) metal coordination : angle 1.40079 ( 4) covalent geometry : bond 0.00290 (12694) covalent geometry : angle 0.51263 (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 66 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 1.253 Fit side-chains REVERT: A 425 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8091 (t0) REVERT: A 602 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7417 (pp20) REVERT: A 699 MET cc_start: 0.7980 (mmm) cc_final: 0.7484 (tpp) REVERT: B 600 HIS cc_start: 0.8764 (t70) cc_final: 0.8454 (m170) REVERT: B 639 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8328 (mm) REVERT: B 697 MET cc_start: 0.9032 (mpp) cc_final: 0.8112 (ptm) REVERT: B 712 ASP cc_start: 0.9262 (t0) cc_final: 0.8743 (p0) outliers start: 19 outliers final: 12 residues processed: 65 average time/residue: 0.1885 time to fit residues: 20.6515 Evaluate side-chains 62 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 725 TRP Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 897 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 53 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 120 optimal weight: 50.0000 chunk 12 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 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 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 = 0.056416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.040323 restraints weight = 85365.017| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 4.56 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12702 Z= 0.209 Angle : 0.557 6.629 17605 Z= 0.280 Chirality : 0.038 0.165 2000 Planarity : 0.004 0.075 1918 Dihedral : 18.593 173.374 2839 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.15 % Allowed : 22.27 % 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: 0.29 (0.24), residues: 1244 helix: 1.76 (0.22), residues: 581 sheet: -0.38 (0.51), residues: 106 loop : -1.45 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 725 HIS 0.004 0.001 HIS A 630 PHE 0.009 0.001 PHE A1163 TYR 0.011 0.001 TYR B 698 ARG 0.006 0.000 ARG C 570 Details of bonding type rmsd hydrogen bonds : bond 0.05946 ( 515) hydrogen bonds : angle 3.86431 ( 1421) metal coordination : bond 0.00862 ( 8) metal coordination : angle 1.29374 ( 4) covalent geometry : bond 0.00475 (12694) covalent geometry : angle 0.55717 (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 72 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 48 time to evaluate : 1.305 Fit side-chains REVERT: A 602 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7529 (pp20) REVERT: A 699 MET cc_start: 0.8115 (mmm) cc_final: 0.7597 (tpp) REVERT: A 1087 GLN cc_start: 0.9504 (OUTLIER) cc_final: 0.9278 (pt0) REVERT: B 600 HIS cc_start: 0.8805 (t70) cc_final: 0.8492 (m170) REVERT: B 639 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8317 (mm) REVERT: B 697 MET cc_start: 0.9061 (mpp) cc_final: 0.8186 (ptm) REVERT: B 712 ASP cc_start: 0.9261 (t0) cc_final: 0.8739 (p0) outliers start: 24 outliers final: 18 residues processed: 71 average time/residue: 0.1966 time to fit residues: 23.5734 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 : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 Chi-restraints excluded: chain C residue 735 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 78 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ** 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 = 0.3776 r_free = 0.3776 target = 0.057176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.041351 restraints weight = 84790.577| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.19 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2449 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= 0.101 Angle : 0.499 7.560 17605 Z= 0.249 Chirality : 0.035 0.167 2000 Planarity : 0.004 0.059 1918 Dihedral : 18.496 172.801 2839 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.88 % Allowed : 22.63 % 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: 0.45 (0.24), residues: 1244 helix: 1.90 (0.22), residues: 580 sheet: -0.34 (0.51), residues: 104 loop : -1.36 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 725 HIS 0.003 0.001 HIS B 600 PHE 0.009 0.001 PHE A1148 TYR 0.008 0.001 TYR B 698 ARG 0.002 0.000 ARG C 570 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 515) hydrogen bonds : angle 3.55368 ( 1421) metal coordination : bond 0.00459 ( 8) metal coordination : angle 1.55200 ( 4) covalent geometry : bond 0.00220 (12694) covalent geometry : angle 0.49856 (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 69 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 1.399 Fit side-chains REVERT: A 425 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8069 (t0) REVERT: A 602 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7460 (pp20) REVERT: B 600 HIS cc_start: 0.8739 (t70) cc_final: 0.8470 (m170) REVERT: B 639 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8317 (mm) REVERT: B 697 MET cc_start: 0.9056 (mpp) cc_final: 0.8198 (ptm) REVERT: B 712 ASP cc_start: 0.9213 (t0) cc_final: 0.8672 (p0) outliers start: 21 outliers final: 14 residues processed: 68 average time/residue: 0.1831 time to fit residues: 20.8469 Evaluate side-chains 65 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 578 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 25 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 89 optimal weight: 0.0040 chunk 56 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 10 optimal weight: 0.1980 overall best weight: 2.5596 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.056608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.040517 restraints weight = 84363.925| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.49 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12702 Z= 0.174 Angle : 0.542 8.652 17605 Z= 0.269 Chirality : 0.037 0.166 2000 Planarity : 0.004 0.059 1918 Dihedral : 18.478 172.958 2839 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.88 % Allowed : 22.45 % 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: 0.42 (0.25), residues: 1244 helix: 1.86 (0.22), residues: 582 sheet: -0.26 (0.51), residues: 106 loop : -1.41 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 725 HIS 0.004 0.001 HIS B 600 PHE 0.008 0.001 PHE A1163 TYR 0.011 0.001 TYR B 698 ARG 0.003 0.000 ARG C 570 Details of bonding type rmsd hydrogen bonds : bond 0.05337 ( 515) hydrogen bonds : angle 3.66432 ( 1421) metal coordination : bond 0.00693 ( 8) metal coordination : angle 1.42930 ( 4) covalent geometry : bond 0.00397 (12694) covalent geometry : angle 0.54121 (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 69 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 1.246 Fit side-chains REVERT: A 425 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8102 (t0) REVERT: A 602 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7511 (pp20) REVERT: B 600 HIS cc_start: 0.8783 (t70) cc_final: 0.8480 (m170) REVERT: B 639 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8240 (mm) REVERT: B 697 MET cc_start: 0.9039 (mpp) cc_final: 0.8160 (ptm) REVERT: B 712 ASP cc_start: 0.9267 (t0) cc_final: 0.8743 (p0) outliers start: 21 outliers final: 17 residues processed: 68 average time/residue: 0.1870 time to fit residues: 21.2344 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 : 1.393 ------------------------------------------------------------------------------- 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 1121 VAL Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1239 THR 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 69 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 0.0270 chunk 58 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.4842 ------------------------------------------------------------------------------- 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 ** 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 = 0.3769 r_free = 0.3769 target = 0.056886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.040731 restraints weight = 83080.136| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.43 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12702 Z= 0.118 Angle : 0.508 8.053 17605 Z= 0.253 Chirality : 0.035 0.167 2000 Planarity : 0.004 0.054 1918 Dihedral : 18.438 172.827 2839 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.97 % Allowed : 22.54 % 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: 0.49 (0.25), residues: 1244 helix: 1.92 (0.22), residues: 581 sheet: -0.17 (0.52), residues: 106 loop : -1.37 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 725 HIS 0.004 0.001 HIS A 802 PHE 0.009 0.001 PHE A1148 TYR 0.010 0.001 TYR B 698 ARG 0.002 0.000 ARG C 570 Details of bonding type rmsd hydrogen bonds : bond 0.04690 ( 515) hydrogen bonds : angle 3.53154 ( 1421) metal coordination : bond 0.00549 ( 8) metal coordination : angle 1.60761 ( 4) covalent geometry : bond 0.00267 (12694) covalent geometry : angle 0.50739 (17601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5164.57 seconds wall clock time: 90 minutes 31.62 seconds (5431.62 seconds total)