Starting phenix.real_space_refine on Fri Jul 3 05:13:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asp_43822/07_2026/9asp_43822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asp_43822/07_2026/9asp_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 { model { file = "/net/cci-nas-00/data/ceres_data/9asp_43822/07_2026/9asp_43822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asp_43822/07_2026/9asp_43822.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9asp_43822/07_2026/9asp_43822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asp_43822/07_2026/9asp_43822.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 2 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Classifications: {'water': 1} Chain breaks: 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: 2.89, per 1000 atoms: 0.24 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: 1.05 Conformation dependent library (CDL) restraints added in 529.2 milliseconds 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: 1.38 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: 2.54 Time building geometry restraints manager: 1.44 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=" N9 A E 108 " pdb=" C4 A E 108 " ideal model delta sigma weight residual 1.374 1.362 0.012 6.00e-03 2.78e+04 3.74e+00 bond pdb=" N7 A E 99 " pdb=" C5 A E 99 " ideal model delta sigma weight residual 1.388 1.378 0.010 6.00e-03 2.78e+04 2.90e+00 bond pdb=" N7 A E 15 " pdb=" C5 A E 15 " ideal model delta sigma weight residual 1.388 1.378 0.010 6.00e-03 2.78e+04 2.54e+00 bond pdb=" C5 A E 104 " pdb=" C4 A E 104 " ideal model delta sigma weight residual 1.383 1.372 0.011 7.00e-03 2.04e+04 2.45e+00 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 ... (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=" C1' U E 94 " pdb=" N1 U E 94 " pdb=" C2 U E 94 " ideal model delta sigma weight residual 117.70 122.10 -4.40 1.20e+00 6.94e-01 1.34e+01 angle pdb=" C1' C E 80 " pdb=" N1 C E 80 " pdb=" C2 C E 80 " ideal model delta sigma weight residual 118.80 122.60 -3.80 1.10e+00 8.26e-01 1.20e+01 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=" N1 C E 80 " pdb=" C2 C E 80 " pdb=" O2 C E 80 " ideal model delta sigma weight residual 118.90 120.78 -1.88 6.00e-01 2.78e+00 9.81e+00 angle pdb=" C1' C E 11 " pdb=" N1 C E 11 " pdb=" C2 C E 11 " ideal model delta sigma weight residual 118.80 122.18 -3.38 1.10e+00 8.26e-01 9.46e+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: 2.790 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.780 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 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= 0.252 Angle : 0.616 8.300 17605 Z= 0.390 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 : 10.47 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (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 ARG 0.011 0.001 ARG B 696 TYR 0.013 0.001 TYR A1199 PHE 0.025 0.001 PHE C 532 TRP 0.035 0.002 TRP A 725 HIS 0.006 0.001 HIS C 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.25 (12694) covalent geometry : angle 0.61623 / 0.39 (17601) hydrogen bonds : bond 0.20577 / 13.94 ( 515) hydrogen bonds : angle 6.14154 / 4.37 ( 1421) metal coordination : bond 0.00925 / 0.57 ( 8) metal coordination : angle 0.58789 / 0.34 ( 4) *********************** 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 : 0.432 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: 0.1029 time to fit residues: 7.6005 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 : 0.440 ------------------------------------------------------------------------------- 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 98 optimal weight: 30.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3755 r_free = 0.3755 target = 0.056756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.040045 restraints weight = 82551.382| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 4.22 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.0761 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= 0.236 Angle : 0.603 8.319 17605 Z= 0.320 Chirality : 0.039 0.156 2000 Planarity : 0.005 0.048 1918 Dihedral : 18.847 176.698 2842 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.95 % Allowed : 21.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.24), residues: 1244 helix: 1.47 (0.22), residues: 569 sheet: -0.50 (0.54), residues: 99 loop : -1.31 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1208 TYR 0.010 0.002 TYR A1332 PHE 0.014 0.001 PHE A1163 TRP 0.014 0.002 TRP A 725 HIS 0.006 0.001 HIS C 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.24 (12694) covalent geometry : angle 0.60298 / 0.32 (17601) hydrogen bonds : bond 0.07575 / 5.14 ( 515) hydrogen bonds : angle 4.73968 / 3.35 ( 1421) metal coordination : bond 0.01120 / 0.70 ( 8) metal coordination : angle 0.74180 / 0.42 ( 4) *********************** 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 79 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 46 time to evaluate : 0.439 Fit side-chains REVERT: A 834 MET cc_start: 0.8522 (ttp) cc_final: 0.8295 (ttt) REVERT: A 935 MET cc_start: 0.8755 (mmp) cc_final: 0.8424 (mmp) outliers start: 33 outliers final: 13 residues processed: 75 average time/residue: 0.0968 time to fit residues: 11.5030 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 : 0.455 ------------------------------------------------------------------------------- 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 875 CYS Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 948 ILE 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 B residue 551 VAL Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 644 VAL 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 126 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 129 optimal weight: 50.0000 chunk 58 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3761 r_free = 0.3761 target = 0.056892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.040110 restraints weight = 82781.231| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 4.26 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1053 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= 0.173 Angle : 0.533 7.704 17605 Z= 0.284 Chirality : 0.037 0.159 2000 Planarity : 0.004 0.049 1918 Dihedral : 18.812 177.427 2842 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.50 % Allowed : 21.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.24), residues: 1244 helix: 1.64 (0.22), residues: 567 sheet: -0.39 (0.54), residues: 99 loop : -1.24 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 570 TYR 0.009 0.001 TYR A1199 PHE 0.013 0.001 PHE B 580 TRP 0.024 0.002 TRP A 725 HIS 0.004 0.001 HIS C 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (12694) covalent geometry : angle 0.53243 / 0.28 (17601) hydrogen bonds : bond 0.06645 / 4.57 ( 515) hydrogen bonds : angle 4.37192 / 3.09 ( 1421) metal coordination : bond 0.00700 / 0.45 ( 8) metal coordination : angle 1.00980 / 0.57 ( 4) *********************** 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 74 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 46 time to evaluate : 0.424 Fit side-chains REVERT: B 712 ASP cc_start: 0.9209 (t0) cc_final: 0.8679 (p0) outliers start: 28 outliers final: 17 residues processed: 72 average time/residue: 0.0900 time to fit residues: 10.4331 Evaluate side-chains 62 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 948 ILE 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 551 VAL Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 643 VAL 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 40 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 101 optimal weight: 0.0670 chunk 111 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3756 r_free = 0.3756 target = 0.056752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.039657 restraints weight = 84166.436| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 4.69 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12702 Z= 0.208 Angle : 0.550 6.022 17605 Z= 0.292 Chirality : 0.038 0.164 2000 Planarity : 0.004 0.050 1918 Dihedral : 18.772 177.286 2839 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.86 % Allowed : 21.82 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.24), residues: 1244 helix: 1.56 (0.22), residues: 573 sheet: -0.47 (0.55), residues: 99 loop : -1.32 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 570 TYR 0.011 0.001 TYR A 784 PHE 0.009 0.001 PHE A1148 TRP 0.026 0.002 TRP A 725 HIS 0.005 0.001 HIS A1238 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (12694) covalent geometry : angle 0.54986 / 0.29 (17601) hydrogen bonds : bond 0.06545 / 4.47 ( 515) hydrogen bonds : angle 4.24279 / 3.00 ( 1421) metal coordination : bond 0.01010 / 0.61 ( 8) metal coordination : angle 1.24399 / 0.70 ( 4) *********************** 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 78 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 46 time to evaluate : 0.420 Fit side-chains REVERT: A 425 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8049 (t0) REVERT: A 602 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7549 (pp20) REVERT: A 939 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.8928 (ttmm) REVERT: A 1087 GLN cc_start: 0.9492 (OUTLIER) cc_final: 0.9283 (pt0) REVERT: B 697 MET cc_start: 0.8961 (mpp) cc_final: 0.7910 (ptm) REVERT: B 712 ASP cc_start: 0.9270 (t0) cc_final: 0.8748 (p0) outliers start: 32 outliers final: 22 residues processed: 76 average time/residue: 0.0894 time to fit residues: 11.0792 Evaluate side-chains 71 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 45 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 632 ILE 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 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 1153 ILE 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 634 MET Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 643 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 122 optimal weight: 40.0000 chunk 106 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 100 optimal weight: 30.0000 chunk 81 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 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 = 0.3762 r_free = 0.3762 target = 0.056865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.039845 restraints weight = 84397.132| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 4.77 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1496 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= 0.170 Angle : 0.516 7.094 17605 Z= 0.274 Chirality : 0.037 0.163 2000 Planarity : 0.004 0.049 1918 Dihedral : 18.767 176.968 2839 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.86 % Allowed : 21.82 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.24), residues: 1244 helix: 1.64 (0.22), residues: 574 sheet: -0.34 (0.55), residues: 99 loop : -1.37 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 570 TYR 0.009 0.001 TYR B 698 PHE 0.010 0.001 PHE A1148 TRP 0.030 0.002 TRP A 725 HIS 0.005 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (12694) covalent geometry : angle 0.51531 / 0.27 (17601) hydrogen bonds : bond 0.06021 / 4.16 ( 515) hydrogen bonds : angle 4.08609 / 2.88 ( 1421) metal coordination : bond 0.00620 / 0.38 ( 8) metal coordination : angle 1.26874 / 0.72 ( 4) *********************** 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: 32 poor density : 45 time to evaluate : 0.441 Fit side-chains REVERT: A 425 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8017 (t0) REVERT: A 939 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.8936 (ttmm) REVERT: A 949 MET cc_start: 0.9001 (mmm) cc_final: 0.8644 (mtm) REVERT: B 712 ASP cc_start: 0.9286 (t0) cc_final: 0.8761 (p0) outliers start: 32 outliers final: 22 residues processed: 75 average time/residue: 0.0926 time to fit residues: 11.2593 Evaluate side-chains 69 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 632 ILE 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 958 THR 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 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 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 576 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 43 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 14 optimal weight: 0.2980 chunk 25 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 30.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** 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 = 0.3776 r_free = 0.3776 target = 0.057328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.040424 restraints weight = 83928.487| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 4.78 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1691 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= 0.102 Angle : 0.482 6.923 17605 Z= 0.255 Chirality : 0.036 0.164 2000 Planarity : 0.004 0.048 1918 Dihedral : 18.713 176.883 2839 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.15 % Allowed : 22.99 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.24), residues: 1244 helix: 1.78 (0.22), residues: 574 sheet: -0.41 (0.54), residues: 99 loop : -1.35 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 663 TYR 0.007 0.001 TYR A1229 PHE 0.011 0.001 PHE C 542 TRP 0.032 0.001 TRP A 725 HIS 0.004 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (12694) covalent geometry : angle 0.48146 / 0.26 (17601) hydrogen bonds : bond 0.05189 / 3.65 ( 515) hydrogen bonds : angle 3.85872 / 2.71 ( 1421) metal coordination : bond 0.00434 / 0.16 ( 8) metal coordination : angle 1.30348 / 0.75 ( 4) *********************** 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 69 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 425 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7943 (t0) REVERT: A 949 MET cc_start: 0.8941 (mmm) cc_final: 0.8526 (mtm) REVERT: B 663 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8866 (mmt-90) REVERT: B 697 MET cc_start: 0.8977 (mpp) cc_final: 0.7980 (ptm) REVERT: B 712 ASP cc_start: 0.9296 (t0) cc_final: 0.8781 (p0) outliers start: 24 outliers final: 13 residues processed: 67 average time/residue: 0.0954 time to fit residues: 9.9833 Evaluate side-chains 60 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 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 642 GLU Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 663 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 30 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 10 optimal weight: 0.0770 chunk 91 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 49 optimal weight: 0.0010 overall best weight: 1.0748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.057343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.039315 restraints weight = 83240.739| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 4.60 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1887 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= 0.104 Angle : 0.475 7.675 17605 Z= 0.249 Chirality : 0.036 0.167 2000 Planarity : 0.004 0.047 1918 Dihedral : 18.600 176.877 2839 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.06 % Allowed : 22.99 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.24), residues: 1244 helix: 1.84 (0.22), residues: 582 sheet: -0.36 (0.53), residues: 99 loop : -1.34 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 663 TYR 0.009 0.001 TYR B 698 PHE 0.010 0.001 PHE A1148 TRP 0.032 0.001 TRP A 725 HIS 0.004 0.001 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (12694) covalent geometry : angle 0.47406 / 0.25 (17601) hydrogen bonds : bond 0.04928 / 3.47 ( 515) hydrogen bonds : angle 3.69362 / 2.60 ( 1421) metal coordination : bond 0.00521 / 0.24 ( 8) metal coordination : angle 1.58792 / 0.92 ( 4) *********************** 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 68 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 425 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7881 (t0) REVERT: A 602 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7473 (pp20) REVERT: B 697 MET cc_start: 0.8830 (mpp) cc_final: 0.7901 (ptm) REVERT: B 712 ASP cc_start: 0.9297 (t0) cc_final: 0.8773 (p0) outliers start: 23 outliers final: 17 residues processed: 66 average time/residue: 0.0786 time to fit residues: 8.6590 Evaluate side-chains 64 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 725 TRP Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 1038 HIS 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 551 VAL Chi-restraints excluded: chain B residue 642 GLU Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 660 HIS 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 73 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 B 687 HIS ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.057077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.040392 restraints weight = 83962.295| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 4.65 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12702 Z= 0.155 Angle : 0.499 7.271 17605 Z= 0.261 Chirality : 0.037 0.167 2000 Planarity : 0.004 0.048 1918 Dihedral : 18.572 176.827 2839 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.15 % Allowed : 23.08 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.24), residues: 1244 helix: 1.84 (0.22), residues: 581 sheet: -0.37 (0.53), residues: 99 loop : -1.32 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 663 TYR 0.011 0.001 TYR A 784 PHE 0.010 0.001 PHE C 542 TRP 0.032 0.001 TRP A 725 HIS 0.015 0.001 HIS B 660 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (12694) covalent geometry : angle 0.49826 / 0.26 (17601) hydrogen bonds : bond 0.05374 / 3.74 ( 515) hydrogen bonds : angle 3.74951 / 2.65 ( 1421) metal coordination : bond 0.00693 / 0.42 ( 8) metal coordination : angle 1.52301 / 0.88 ( 4) *********************** 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 69 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 425 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7949 (t0) REVERT: A 602 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7455 (pp20) REVERT: B 600 HIS cc_start: 0.8734 (t70) cc_final: 0.8431 (m170) REVERT: B 634 MET cc_start: 0.3541 (OUTLIER) cc_final: 0.3041 (mmp) REVERT: B 697 MET cc_start: 0.8994 (mpp) cc_final: 0.7874 (ptm) REVERT: B 712 ASP cc_start: 0.9230 (t0) cc_final: 0.8700 (p0) outliers start: 24 outliers final: 20 residues processed: 66 average time/residue: 0.0837 time to fit residues: 9.2750 Evaluate side-chains 68 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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 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 551 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 642 GLU Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain C residue 516 LEU 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 89 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 129 optimal weight: 50.0000 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 ASN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.057307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.039456 restraints weight = 83260.843| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 4.30 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12702 Z= 0.109 Angle : 0.475 7.544 17605 Z= 0.248 Chirality : 0.036 0.166 2000 Planarity : 0.003 0.048 1918 Dihedral : 18.563 176.629 2839 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.06 % Allowed : 23.43 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.24), residues: 1244 helix: 1.88 (0.22), residues: 582 sheet: -0.29 (0.53), residues: 99 loop : -1.30 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 663 TYR 0.008 0.001 TYR C 530 PHE 0.009 0.001 PHE A 970 TRP 0.033 0.001 TRP A 725 HIS 0.004 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (12694) covalent geometry : angle 0.47452 / 0.25 (17601) hydrogen bonds : bond 0.04931 / 3.49 ( 515) hydrogen bonds : angle 3.64689 / 2.57 ( 1421) metal coordination : bond 0.00437 / 0.20 ( 8) metal coordination : angle 1.37166 / 0.80 ( 4) *********************** 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 68 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 425 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7838 (t0) REVERT: A 602 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7471 (pp20) REVERT: A 939 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8840 (ttmm) REVERT: B 600 HIS cc_start: 0.8803 (t70) cc_final: 0.8466 (m170) REVERT: B 634 MET cc_start: 0.3356 (OUTLIER) cc_final: 0.2862 (mmp) REVERT: B 697 MET cc_start: 0.8909 (mpp) cc_final: 0.7960 (ptm) REVERT: B 712 ASP cc_start: 0.9304 (t0) cc_final: 0.8846 (p0) outliers start: 23 outliers final: 19 residues processed: 65 average time/residue: 0.0896 time to fit residues: 9.6415 Evaluate side-chains 68 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 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 1237 VAL 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 581 VAL Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 642 GLU Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 660 HIS 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 22 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 95 optimal weight: 0.0980 chunk 1 optimal weight: 0.0970 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** 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 = 0.3779 r_free = 0.3779 target = 0.057356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.039591 restraints weight = 83751.573| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 4.38 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2070 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= 0.104 Angle : 0.477 7.949 17605 Z= 0.247 Chirality : 0.035 0.167 2000 Planarity : 0.003 0.047 1918 Dihedral : 18.546 176.505 2839 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.15 % Allowed : 23.35 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1244 helix: 1.89 (0.22), residues: 582 sheet: -0.22 (0.53), residues: 99 loop : -1.29 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 663 TYR 0.008 0.001 TYR B 698 PHE 0.010 0.001 PHE C 542 TRP 0.033 0.001 TRP A 725 HIS 0.005 0.001 HIS B 660 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (12694) covalent geometry : angle 0.47642 / 0.25 (17601) hydrogen bonds : bond 0.04934 / 3.48 ( 515) hydrogen bonds : angle 3.62378 / 2.56 ( 1421) metal coordination : bond 0.00423 / 0.19 ( 8) metal coordination : angle 1.43969 / 0.84 ( 4) ********************** 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: 24 poor density : 45 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 425 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7764 (t0) REVERT: A 602 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7488 (pp20) REVERT: A 939 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8843 (ttmm) REVERT: B 600 HIS cc_start: 0.8817 (t70) cc_final: 0.8484 (m170) REVERT: B 697 MET cc_start: 0.8880 (mpp) cc_final: 0.7964 (ptm) REVERT: B 712 ASP cc_start: 0.9294 (t0) cc_final: 0.8812 (p0) outliers start: 24 outliers final: 20 residues processed: 66 average time/residue: 0.0888 time to fit residues: 9.6596 Evaluate side-chains 68 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 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 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 551 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 642 GLU Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 660 HIS 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 121 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 129 optimal weight: 50.0000 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 113 optimal weight: 0.0030 chunk 26 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** 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 = 0.3770 r_free = 0.3770 target = 0.057036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.039223 restraints weight = 83302.427| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 4.48 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12702 Z= 0.157 Angle : 0.498 7.761 17605 Z= 0.257 Chirality : 0.036 0.167 2000 Planarity : 0.004 0.048 1918 Dihedral : 18.524 176.404 2839 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.15 % Allowed : 23.26 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.24), residues: 1244 helix: 1.88 (0.22), residues: 582 sheet: -0.26 (0.53), residues: 99 loop : -1.30 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 663 TYR 0.011 0.001 TYR A 784 PHE 0.009 0.001 PHE A1148 TRP 0.033 0.001 TRP A 725 HIS 0.006 0.001 HIS B 660 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (12694) covalent geometry : angle 0.49749 / 0.26 (17601) hydrogen bonds : bond 0.05294 / 3.69 ( 515) hydrogen bonds : angle 3.68482 / 2.61 ( 1421) metal coordination : bond 0.00703 / 0.43 ( 8) metal coordination : angle 1.56194 / 0.90 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2620.45 seconds wall clock time: 45 minutes 58.31 seconds (2758.31 seconds total)