Starting phenix.real_space_refine on Sat Sep 12 18:52:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ryr_10058/09_2026/6ryr_10058.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ryr_10058/09_2026/6ryr_10058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ryr_10058/09_2026/6ryr_10058.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ryr_10058/09_2026/6ryr_10058.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ryr_10058/09_2026/6ryr_10058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ryr_10058/09_2026/6ryr_10058.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ryr_10058/09_2026/6ryr_10058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ryr_10058/09_2026/6ryr_10058.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 300 5.49 5 Mg 1 5.21 5 S 56 5.16 5 C 10325 2.51 5 N 3271 2.21 5 O 3879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17834 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3036 Classifications: {'DNA': 149} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 148} Chain: "J" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3070 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "W" Number of atoms: 5634 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 696, 5620 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 30, 'TRANS': 665} Chain breaks: 3 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 43 Conformer: "B" Number of residues, atoms: 696, 5620 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 30, 'TRANS': 665} Chain breaks: 3 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 43 bond proxies already assigned to first conformer: 5745 Chain: "W" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 94 Unusual residues: {' MG': 1, ' ZN': 2, 'ANP': 1} Classifications: {'peptide': 12, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11, None: 4} Not linked: pdbres="UNK W1212 " pdbres="ANP W2001 " Not linked: pdbres="ANP W2001 " pdbres=" MG W2002 " Not linked: pdbres=" MG W2002 " pdbres=" ZN W2003 " Not linked: pdbres=" ZN W2003 " pdbres=" ZN W2004 " Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12168 SG CYS W 452 53.151 106.010 51.790 1.00119.90 S ATOM 12192 SG CYS W 455 56.142 106.266 52.974 1.00121.24 S ATOM 12340 SG CYS W 475 55.878 107.234 49.266 1.00122.47 S ATOM 12254 SG CYS W 464 39.798 107.120 48.607 1.00120.66 S ATOM 12275 SG CYS W 467 40.507 103.969 49.929 1.00120.83 S ATOM 12458 SG CYS W 490 42.907 104.215 47.121 1.00118.60 S ATOM 12482 SG CYS W 493 39.702 104.419 46.627 1.00115.34 S Time building chain proxies: 4.53, per 1000 atoms: 0.25 Number of scatterers: 17834 At special positions: 0 Unit cell: (97.65, 129.15, 154.35, 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 S 56 16.00 P 300 15.00 Mg 1 11.99 O 3879 8.00 N 3271 7.00 C 10325 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: 1.51 Conformation dependent library (CDL) restraints added in 710.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN W2003 " pdb="ZN ZN W2003 " - pdb=" SG CYS W 455 " pdb="ZN ZN W2003 " - pdb=" SG CYS W 475 " pdb="ZN ZN W2003 " - pdb=" SG CYS W 452 " pdb=" ZN W2004 " pdb="ZN ZN W2004 " - pdb=" SG CYS W 467 " pdb="ZN ZN W2004 " - pdb=" SG CYS W 493 " pdb="ZN ZN W2004 " - pdb=" SG CYS W 490 " pdb="ZN ZN W2004 " - pdb=" SG CYS W 464 " Number of angles added : 6 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 16 sheets defined 58.4% alpha, 7.1% beta 110 base pairs and 270 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.724A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.605A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.728A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.521A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.555A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 102 through 121 removed outlier: 3.817A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.963A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 75 removed outlier: 3.808A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.606A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.919A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 551 through 555 removed outlier: 3.552A pdb=" N CYS W 555 " --> pdb=" O TYR W 552 " (cutoff:3.500A) Processing helix chain 'W' and resid 560 through 566 removed outlier: 3.660A pdb=" N LEU W 565 " --> pdb=" O LEU W 561 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS W 566 " --> pdb=" O GLN W 562 " (cutoff:3.500A) Processing helix chain 'W' and resid 567 through 578 removed outlier: 3.511A pdb=" N PHE W 571 " --> pdb=" O CYS W 567 " (cutoff:3.500A) Processing helix chain 'W' and resid 593 through 599 Processing helix chain 'W' and resid 602 through 612 removed outlier: 3.679A pdb=" N GLU W 610 " --> pdb=" O ALA W 606 " (cutoff:3.500A) Processing helix chain 'W' and resid 613 through 616 Processing helix chain 'W' and resid 618 through 622 Processing helix chain 'W' and resid 648 through 652 Processing helix chain 'W' and resid 663 through 678 removed outlier: 3.632A pdb=" N PHE W 667 " --> pdb=" O ASP W 663 " (cutoff:3.500A) Processing helix chain 'W' and resid 716 through 721 removed outlier: 3.711A pdb=" N ASP W 720 " --> pdb=" O PRO W 716 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA W 721 " --> pdb=" O GLU W 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 716 through 721' Processing helix chain 'W' and resid 727 through 743 removed outlier: 3.812A pdb=" N GLN W 743 " --> pdb=" O PHE W 739 " (cutoff:3.500A) Processing helix chain 'W' and resid 756 through 772 removed outlier: 3.621A pdb=" N GLY W 772 " --> pdb=" O LEU W 768 " (cutoff:3.500A) Processing helix chain 'W' and resid 783 through 785 No H-bonds generated for 'chain 'W' and resid 783 through 785' Processing helix chain 'W' and resid 786 through 791 Processing helix chain 'W' and resid 809 through 821 removed outlier: 3.795A pdb=" N PHE W 821 " --> pdb=" O ARG W 817 " (cutoff:3.500A) Processing helix chain 'W' and resid 852 through 858 removed outlier: 4.131A pdb=" N THR W 856 " --> pdb=" O TYR W 852 " (cutoff:3.500A) Processing helix chain 'W' and resid 862 through 866 removed outlier: 4.224A pdb=" N ASP W 866 " --> pdb=" O GLY W 863 " (cutoff:3.500A) Processing helix chain 'W' and resid 875 through 878 Processing helix chain 'W' and resid 883 through 892 removed outlier: 3.764A pdb=" N GLY W 891 " --> pdb=" O ARG W 887 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR W 892 " --> pdb=" O VAL W 888 " (cutoff:3.500A) Processing helix chain 'W' and resid 909 through 920 Processing helix chain 'W' and resid 927 through 931 Processing helix chain 'W' and resid 938 through 950 removed outlier: 4.117A pdb=" N LYS W 944 " --> pdb=" O GLU W 940 " (cutoff:3.500A) Processing helix chain 'W' and resid 979 through 991 removed outlier: 3.651A pdb=" N TYR W 985 " --> pdb=" O MET W 981 " (cutoff:3.500A) Processing helix chain 'W' and resid 993 through 998 Processing helix chain 'W' and resid 1010 through 1021 removed outlier: 3.673A pdb=" N ASP W1014 " --> pdb=" O ASN W1010 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS W1016 " --> pdb=" O VAL W1012 " (cutoff:3.500A) Processing helix chain 'W' and resid 1022 through 1024 No H-bonds generated for 'chain 'W' and resid 1022 through 1024' Processing helix chain 'W' and resid 1025 through 1031 Processing helix chain 'W' and resid 1041 through 1048 Processing helix chain 'W' and resid 1049 through 1066 removed outlier: 3.699A pdb=" N LEU W1053 " --> pdb=" O SER W1049 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU W1054 " --> pdb=" O GLY W1050 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN W1061 " --> pdb=" O LYS W1057 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU W1064 " --> pdb=" O LYS W1060 " (cutoff:3.500A) Processing helix chain 'W' and resid 1077 through 1090 removed outlier: 3.515A pdb=" N LEU W1081 " --> pdb=" O LYS W1077 " (cutoff:3.500A) Processing helix chain 'W' and resid 1101 through 1113 Processing helix chain 'W' and resid 1150 through 1158 removed outlier: 3.987A pdb=" N ALA W1156 " --> pdb=" O ASN W1152 " (cutoff:3.500A) Processing helix chain 'W' and resid 1179 through 1192 removed outlier: 3.802A pdb=" N ARG W1183 " --> pdb=" O SER W1179 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET W1192 " --> pdb=" O ALA W1188 " (cutoff:3.500A) Processing helix chain 'W' and resid 1202 through 1210 removed outlier: 3.691A pdb=" N UNK W1206 " --> pdb=" O UNK W1202 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N UNK W1208 " --> pdb=" O UNK W1204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.034A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.406A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.253A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.660A pdb=" N TYR F 98 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.284A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.440A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'W' and resid 462 through 463 Processing sheet with id=AB3, first strand: chain 'W' and resid 502 through 510 removed outlier: 3.557A pdb=" N LYS W 504 " --> pdb=" O LYS W 546 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE W 544 " --> pdb=" O LEU W 506 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TRP W 508 " --> pdb=" O GLN W 542 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN W 542 " --> pdb=" O TRP W 508 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL W 545 " --> pdb=" O SER W 556 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER W 556 " --> pdb=" O VAL W 545 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'W' and resid 624 through 631 removed outlier: 6.886A pdb=" N LYS W 643 " --> pdb=" O HIS W 625 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE W 627 " --> pdb=" O LEU W 641 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU W 641 " --> pdb=" O ILE W 627 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN W 629 " --> pdb=" O HIS W 639 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N HIS W 639 " --> pdb=" O ASN W 629 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'W' and resid 747 through 748 removed outlier: 6.942A pdb=" N THR W 747 " --> pdb=" O LEU W 899 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU W 870 " --> pdb=" O LEU W 898 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU W 900 " --> pdb=" O LEU W 870 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL W 872 " --> pdb=" O LEU W 900 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU W 779 " --> pdb=" O ILE W 871 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP W 873 " --> pdb=" O LEU W 779 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SER W 781 " --> pdb=" O ASP W 873 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER W 851 " --> pdb=" O TYR W 806 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'W' and resid 969 through 976 removed outlier: 6.266A pdb=" N THR W 970 " --> pdb=" O ILE W1171 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ARG W1173 " --> pdb=" O THR W 970 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU W 972 " --> pdb=" O ARG W1173 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL W1175 " --> pdb=" O LEU W 972 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL W 974 " --> pdb=" O VAL W1175 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU W1070 " --> pdb=" O ILE W1142 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL W1069 " --> pdb=" O PHE W1122 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU W1124 " --> pdb=" O VAL W1069 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE W1071 " --> pdb=" O LEU W1124 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU W1094 " --> pdb=" O LEU W1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'W' and resid 1034 through 1035 removed outlier: 3.795A pdb=" N MET W1039 " --> pdb=" O MET W1035 " (cutoff:3.500A) 571 hydrogen bonds defined for protein. 1671 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 273 hydrogen bonds 546 hydrogen bond angles 0 basepair planarities 110 basepair parallelities 270 stacking parallelities Total time for adding SS restraints: 5.37 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4272 1.33 - 1.45: 4895 1.45 - 1.57: 8937 1.57 - 1.69: 599 1.69 - 1.81: 95 Bond restraints: 18798 Sorted by residual: bond pdb=" O3A ANP W2001 " pdb=" PB ANP W2001 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" N3B ANP W2001 " pdb=" PG ANP W2001 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C1' DT J -73 " pdb=" N1 DT J -73 " ideal model delta sigma weight residual 1.468 1.526 -0.058 1.40e-02 5.10e+03 1.69e+01 bond pdb=" C1' DC J 58 " pdb=" N1 DC J 58 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.44e+01 bond pdb=" O5' ANP W2001 " pdb=" PA ANP W2001 " ideal model delta sigma weight residual 1.655 1.581 0.074 2.00e-02 2.50e+03 1.35e+01 ... (remaining 18793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 26603 3.69 - 7.39: 69 7.39 - 11.08: 5 11.08 - 14.77: 1 14.77 - 18.47: 1 Bond angle restraints: 26679 Sorted by residual: angle pdb=" PB ANP W2001 " pdb=" N3B ANP W2001 " pdb=" PG ANP W2001 " ideal model delta sigma weight residual 126.95 108.48 18.47 3.00e+00 1.11e-01 3.79e+01 angle pdb=" N3 DT J -65 " pdb=" C4 DT J -65 " pdb=" O4 DT J -65 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT J 33 " pdb=" C4 DT J 33 " pdb=" O4 DT J 33 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT I 30 " pdb=" C4 DT I 30 " pdb=" O4 DT I 30 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT I -26 " pdb=" C4 DT I -26 " pdb=" O4 DT I -26 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 ... (remaining 26674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 9209 34.91 - 69.82: 1273 69.82 - 104.73: 32 104.73 - 139.64: 0 139.64 - 174.55: 1 Dihedral angle restraints: 10515 sinusoidal: 6252 harmonic: 4263 Sorted by residual: dihedral pdb=" CA LYS W 546 " pdb=" C LYS W 546 " pdb=" N TRP W 547 " pdb=" CA TRP W 547 " ideal model delta harmonic sigma weight residual -180.00 -157.08 -22.92 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 45.45 174.55 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ASN W1004 " pdb=" C ASN W1004 " pdb=" N GLN W1005 " pdb=" CA GLN W1005 " ideal model delta harmonic sigma weight residual 180.00 161.21 18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 10512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.355: 2974 0.355 - 0.709: 0 0.709 - 1.064: 0 1.064 - 1.419: 0 1.419 - 1.773: 1 Chirality restraints: 2975 Sorted by residual: chirality pdb=" CG LEU W 480 " pdb=" CB LEU W 480 " pdb=" CD1 LEU W 480 " pdb=" CD2 LEU W 480 " both_signs ideal model delta sigma weight residual False -2.59 -0.82 -1.77 2.00e-01 2.50e+01 7.86e+01 chirality pdb=" C3' ANP W2001 " pdb=" C2' ANP W2001 " pdb=" C4' ANP W2001 " pdb=" O3' ANP W2001 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C3' DA I 61 " pdb=" C4' DA I 61 " pdb=" O3' DA I 61 " pdb=" C2' DA I 61 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.46e-01 ... (remaining 2972 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN W 477 " -0.046 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO W 478 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO W 478 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO W 478 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA J -72 " 0.033 2.00e-02 2.50e+03 1.44e-02 5.73e+00 pdb=" N9 DA J -72 " -0.031 2.00e-02 2.50e+03 pdb=" C8 DA J -72 " -0.009 2.00e-02 2.50e+03 pdb=" N7 DA J -72 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA J -72 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA J -72 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA J -72 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA J -72 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA J -72 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA J -72 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DA J -72 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY W 951 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO W 952 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO W 952 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO W 952 " -0.032 5.00e-02 4.00e+02 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 76 2.49 - 3.10: 11957 3.10 - 3.70: 28106 3.70 - 4.30: 43965 4.30 - 4.90: 66938 Nonbonded interactions: 151042 Sorted by model distance: nonbonded pdb=" OH TYR W 852 " pdb=" O ASP W 873 " model vdw 1.893 3.040 nonbonded pdb=" OD2 ASP A 81 " pdb=" NH2 ARG W 992 " model vdw 2.123 3.120 nonbonded pdb=" O ASN W1037 " pdb=" ND2 ASN W1037 " model vdw 2.148 3.120 nonbonded pdb=" O2G ANP W2001 " pdb="MG MG W2002 " model vdw 2.153 2.170 nonbonded pdb=" N3B ANP W2001 " pdb="MG MG W2002 " model vdw 2.175 2.250 ... (remaining 151037 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } 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=0.50 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: 0.210 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 23.240 Find NCS groups from input model: 0.170 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.197 18805 Z= 0.440 Angle : 0.834 43.094 26685 Z= 0.590 Chirality : 0.064 1.773 2975 Planarity : 0.004 0.069 2352 Dihedral : 23.864 174.551 7763 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.16 % Allowed : 0.41 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.22), residues: 1429 helix: 0.84 (0.19), residues: 781 sheet: -0.45 (0.54), residues: 91 loop : -1.34 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 128 TYR 0.029 0.002 TYR W 664 PHE 0.024 0.002 PHE W 885 TRP 0.017 0.002 TRP W 621 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.44 (18798) covalent geometry : angle 0.76918 / 0.59 (26679) hydrogen bonds : bond 0.17644 / 11.93 ( 844) hydrogen bonds : angle 5.90608 / 4.44 ( 2217) metal coordination : bond 0.09063 / 5.72 ( 7) metal coordination : angle 21.59820 / 14.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 181 time to evaluate : 0.426 Fit side-chains REVERT: B 16 LYS cc_start: 0.5215 (OUTLIER) cc_final: 0.4692 (ptpp) REVERT: C 36 LYS cc_start: 0.8277 (mmtm) cc_final: 0.8052 (mptt) REVERT: W 622 MET cc_start: 0.8273 (mmm) cc_final: 0.7811 (mmm) REVERT: W 1091 TYR cc_start: 0.7849 (m-10) cc_final: 0.7563 (m-10) REVERT: W 1193 MET cc_start: 0.6195 (mmt) cc_final: 0.5846 (ptt) outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 0.1748 time to fit residues: 45.6156 Evaluate side-chains 161 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.5980 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 93 GLN A 113 HIS B 64 ASN B 75 HIS D 44 GLN D 81 ASN E 39 HIS H 92 GLN H 106 HIS W 573 ASN W 914 HIS W1037 ASN W1151 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.142903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.109793 restraints weight = 40202.442| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.59 r_work: 0.3256 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18805 Z= 0.172 Angle : 0.753 11.478 26685 Z= 0.421 Chirality : 0.048 0.214 2975 Planarity : 0.006 0.062 2352 Dihedral : 27.053 179.102 4880 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.06 % Allowed : 8.71 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.22), residues: 1429 helix: 1.20 (0.19), residues: 798 sheet: -0.44 (0.55), residues: 91 loop : -1.14 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG W 738 TYR 0.025 0.002 TYR W 712 PHE 0.026 0.002 PHE W 913 TRP 0.024 0.002 TRP W 547 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (18798) covalent geometry : angle 0.74484 / 0.42 (26679) hydrogen bonds : bond 0.06158 / 4.25 ( 844) hydrogen bonds : angle 3.78194 / 2.75 ( 2217) metal coordination : bond 0.01316 / 0.55 ( 7) metal coordination : angle 7.23075 / 4.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.523 Fit side-chains REVERT: B 16 LYS cc_start: 0.4647 (OUTLIER) cc_final: 0.4349 (ptpt) REVERT: F 84 MET cc_start: 0.7576 (mmm) cc_final: 0.7327 (mmm) REVERT: W 548 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7385 (mt0) REVERT: W 966 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6691 (tmm) REVERT: W 1091 TYR cc_start: 0.8205 (m-10) cc_final: 0.7810 (m-10) REVERT: W 1193 MET cc_start: 0.6457 (mmt) cc_final: 0.5700 (ptt) outliers start: 13 outliers final: 3 residues processed: 160 average time/residue: 0.1548 time to fit residues: 36.8195 Evaluate side-chains 151 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain W residue 548 GLN Chi-restraints excluded: chain W residue 966 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 7 optimal weight: 0.5980 chunk 124 optimal weight: 0.6980 chunk 71 optimal weight: 30.0000 chunk 111 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN ** W 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 998 ASN W1037 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.142537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.108750 restraints weight = 47160.306| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.73 r_work: 0.3238 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18805 Z= 0.144 Angle : 0.615 11.368 26685 Z= 0.356 Chirality : 0.042 0.178 2975 Planarity : 0.005 0.066 2352 Dihedral : 27.668 177.747 4880 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.22 % Allowed : 10.98 % Favored : 87.79 % 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: 0.63 (0.22), residues: 1429 helix: 1.56 (0.19), residues: 794 sheet: -0.30 (0.57), residues: 88 loop : -1.18 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG W 817 TYR 0.018 0.001 TYR W 574 PHE 0.016 0.001 PHE W 913 TRP 0.010 0.001 TRP W 553 HIS 0.003 0.001 HIS W 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (18798) covalent geometry : angle 0.61190 / 0.36 (26679) hydrogen bonds : bond 0.05249 / 3.54 ( 844) hydrogen bonds : angle 3.46910 / 2.53 ( 2217) metal coordination : bond 0.00709 / 0.31 ( 7) metal coordination : angle 4.16690 / 2.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: B 16 LYS cc_start: 0.4676 (OUTLIER) cc_final: 0.4364 (ptpt) REVERT: D 90 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: W 560 GLU cc_start: 0.7195 (pp20) cc_final: 0.6888 (pt0) REVERT: W 719 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8680 (tp) REVERT: W 981 MET cc_start: 0.8213 (tmm) cc_final: 0.7927 (tmm) REVERT: W 1091 TYR cc_start: 0.8265 (m-10) cc_final: 0.7849 (m-10) REVERT: W 1193 MET cc_start: 0.6554 (mmt) cc_final: 0.5678 (ptt) outliers start: 15 outliers final: 7 residues processed: 165 average time/residue: 0.1540 time to fit residues: 37.6183 Evaluate side-chains 150 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain W residue 510 TRP Chi-restraints excluded: chain W residue 570 MET Chi-restraints excluded: chain W residue 719 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 114 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN D 44 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** W 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1037 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.136993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102258 restraints weight = 41254.557| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.63 r_work: 0.3140 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 18805 Z= 0.258 Angle : 0.713 9.840 26685 Z= 0.394 Chirality : 0.048 0.193 2975 Planarity : 0.006 0.100 2352 Dihedral : 28.206 177.916 4880 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.28 % Allowed : 12.21 % Favored : 85.52 % 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: 0.32 (0.22), residues: 1429 helix: 1.33 (0.18), residues: 795 sheet: -0.54 (0.52), residues: 104 loop : -1.35 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 30 TYR 0.020 0.002 TYR W 712 PHE 0.020 0.002 PHE W 886 TRP 0.009 0.002 TRP W 672 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.26 (18798) covalent geometry : angle 0.70945 / 0.39 (26679) hydrogen bonds : bond 0.06187 / 4.15 ( 844) hydrogen bonds : angle 3.64756 / 2.65 ( 2217) metal coordination : bond 0.02203 / 1.34 ( 7) metal coordination : angle 4.58186 / 2.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.547 Fit side-chains REVERT: B 16 LYS cc_start: 0.4719 (OUTLIER) cc_final: 0.4400 (ptpt) REVERT: H 56 MET cc_start: 0.8688 (tpp) cc_final: 0.8405 (tpp) REVERT: W 548 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7821 (mt0) REVERT: W 1091 TYR cc_start: 0.8303 (m-10) cc_final: 0.7919 (m-10) REVERT: W 1193 MET cc_start: 0.6768 (mmt) cc_final: 0.5907 (ptt) outliers start: 28 outliers final: 17 residues processed: 161 average time/residue: 0.1504 time to fit residues: 36.4024 Evaluate side-chains 152 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain W residue 510 TRP Chi-restraints excluded: chain W residue 548 GLN Chi-restraints excluded: chain W residue 570 MET Chi-restraints excluded: chain W residue 719 LEU Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 809 ASP Chi-restraints excluded: chain W residue 837 MET Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 954 MET Chi-restraints excluded: chain W residue 1046 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 59 optimal weight: 0.9980 chunk 120 optimal weight: 0.0170 chunk 85 optimal weight: 40.0000 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 669 GLN W1037 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.139074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104321 restraints weight = 50123.355| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.86 r_work: 0.3160 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18805 Z= 0.148 Angle : 0.636 11.441 26685 Z= 0.360 Chirality : 0.044 0.232 2975 Planarity : 0.005 0.075 2352 Dihedral : 28.134 176.957 4880 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.03 % Allowed : 13.26 % Favored : 84.70 % 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: 0.62 (0.22), residues: 1429 helix: 1.59 (0.19), residues: 796 sheet: -0.55 (0.51), residues: 104 loop : -1.23 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 30 TYR 0.017 0.002 TYR W 712 PHE 0.020 0.002 PHE W 913 TRP 0.010 0.001 TRP W 621 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (18798) covalent geometry : angle 0.63394 / 0.36 (26679) hydrogen bonds : bond 0.05174 / 3.46 ( 844) hydrogen bonds : angle 3.51508 / 2.55 ( 2217) metal coordination : bond 0.00745 / 0.37 ( 7) metal coordination : angle 3.58430 / 2.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.558 Fit side-chains REVERT: A 112 ILE cc_start: 0.9581 (OUTLIER) cc_final: 0.9348 (mt) REVERT: B 16 LYS cc_start: 0.4652 (OUTLIER) cc_final: 0.4257 (ptpt) REVERT: D 90 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: H 68 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7279 (mm-30) REVERT: W 560 GLU cc_start: 0.7332 (pp20) cc_final: 0.6937 (pt0) REVERT: W 1030 MET cc_start: 0.8307 (tpp) cc_final: 0.7898 (mmp) REVERT: W 1091 TYR cc_start: 0.8339 (m-10) cc_final: 0.8002 (m-10) REVERT: W 1193 MET cc_start: 0.6680 (mmt) cc_final: 0.5784 (ptt) outliers start: 25 outliers final: 15 residues processed: 155 average time/residue: 0.1523 time to fit residues: 35.3462 Evaluate side-chains 154 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain W residue 510 TRP Chi-restraints excluded: chain W residue 570 MET Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 811 ASP Chi-restraints excluded: chain W residue 837 MET Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 950 LEU Chi-restraints excluded: chain W residue 1046 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 120 optimal weight: 0.0170 chunk 164 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 472 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 = 0.3878 r_free = 0.3878 target = 0.140047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.106649 restraints weight = 33669.131| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.37 r_work: 0.3239 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18805 Z= 0.133 Angle : 0.609 11.432 26685 Z= 0.348 Chirality : 0.042 0.177 2975 Planarity : 0.005 0.081 2352 Dihedral : 28.055 176.309 4880 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.87 % Allowed : 13.83 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.83 (0.22), residues: 1429 helix: 1.75 (0.19), residues: 796 sheet: -0.30 (0.55), residues: 94 loop : -1.16 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 30 TYR 0.020 0.001 TYR W 712 PHE 0.017 0.001 PHE W 913 TRP 0.007 0.001 TRP W 553 HIS 0.005 0.001 HIS W 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 (18798) covalent geometry : angle 0.60717 / 0.35 (26679) hydrogen bonds : bond 0.04751 / 3.19 ( 844) hydrogen bonds : angle 3.39184 / 2.46 ( 2217) metal coordination : bond 0.00511 / 0.22 ( 7) metal coordination : angle 2.88297 / 1.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.529 Fit side-chains REVERT: A 112 ILE cc_start: 0.9586 (OUTLIER) cc_final: 0.9347 (mt) REVERT: B 16 LYS cc_start: 0.4582 (OUTLIER) cc_final: 0.4220 (ptpt) REVERT: D 90 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: W 473 ILE cc_start: 0.3421 (OUTLIER) cc_final: 0.3134 (tp) REVERT: W 560 GLU cc_start: 0.7254 (pp20) cc_final: 0.6925 (pt0) REVERT: W 623 MET cc_start: 0.8152 (ptp) cc_final: 0.7396 (pmm) REVERT: W 1030 MET cc_start: 0.8404 (tpp) cc_final: 0.8014 (mmp) REVERT: W 1193 MET cc_start: 0.6732 (mmt) cc_final: 0.5852 (ptt) outliers start: 23 outliers final: 14 residues processed: 163 average time/residue: 0.1392 time to fit residues: 34.8845 Evaluate side-chains 156 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain W residue 473 ILE Chi-restraints excluded: chain W residue 510 TRP Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 803 VAL Chi-restraints excluded: chain W residue 809 ASP Chi-restraints excluded: chain W residue 811 ASP Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 1046 ILE Chi-restraints excluded: chain W residue 1069 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 115 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 573 ASN W1037 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.138258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103447 restraints weight = 43079.833| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.64 r_work: 0.3151 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18805 Z= 0.200 Angle : 0.640 10.398 26685 Z= 0.359 Chirality : 0.044 0.179 2975 Planarity : 0.005 0.099 2352 Dihedral : 28.248 175.738 4880 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.20 % Allowed : 14.89 % Favored : 82.91 % 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: 0.67 (0.22), residues: 1429 helix: 1.63 (0.19), residues: 797 sheet: -0.49 (0.52), residues: 104 loop : -1.22 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 30 TYR 0.020 0.002 TYR H 39 PHE 0.017 0.002 PHE W 886 TRP 0.008 0.001 TRP W 867 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (18798) covalent geometry : angle 0.63793 / 0.36 (26679) hydrogen bonds : bond 0.05309 / 3.55 ( 844) hydrogen bonds : angle 3.49223 / 2.52 ( 2217) metal coordination : bond 0.00610 / 0.25 ( 7) metal coordination : angle 3.17352 / 1.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.448 Fit side-chains REVERT: A 112 ILE cc_start: 0.9573 (OUTLIER) cc_final: 0.9336 (mt) REVERT: B 16 LYS cc_start: 0.4704 (OUTLIER) cc_final: 0.4306 (ptpt) REVERT: D 90 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: W 473 ILE cc_start: 0.3070 (OUTLIER) cc_final: 0.2771 (tp) REVERT: W 560 GLU cc_start: 0.7289 (pp20) cc_final: 0.6950 (pt0) REVERT: W 623 MET cc_start: 0.8160 (ptp) cc_final: 0.7287 (pmm) REVERT: W 1193 MET cc_start: 0.6674 (mmt) cc_final: 0.5881 (ptt) outliers start: 27 outliers final: 17 residues processed: 154 average time/residue: 0.1432 time to fit residues: 33.1943 Evaluate side-chains 154 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain W residue 473 ILE Chi-restraints excluded: chain W residue 510 TRP Chi-restraints excluded: chain W residue 570 MET Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 803 VAL Chi-restraints excluded: chain W residue 809 ASP Chi-restraints excluded: chain W residue 811 ASP Chi-restraints excluded: chain W residue 849 LEU Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 1046 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 146 optimal weight: 0.9990 chunk 85 optimal weight: 40.0000 chunk 84 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 134 optimal weight: 0.4980 chunk 157 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 142 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 472 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 = 0.3875 r_free = 0.3875 target = 0.139638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.104931 restraints weight = 44253.558| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.67 r_work: 0.3184 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18805 Z= 0.127 Angle : 0.611 11.965 26685 Z= 0.346 Chirality : 0.043 0.350 2975 Planarity : 0.005 0.090 2352 Dihedral : 28.195 175.909 4880 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.79 % Allowed : 15.22 % Favored : 82.99 % 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: 0.87 (0.22), residues: 1429 helix: 1.80 (0.19), residues: 797 sheet: -0.48 (0.51), residues: 104 loop : -1.11 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 30 TYR 0.017 0.002 TYR H 39 PHE 0.018 0.002 PHE W 913 TRP 0.008 0.001 TRP W 736 HIS 0.005 0.001 HIS W 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.13 (18798) covalent geometry : angle 0.60946 / 0.35 (26679) hydrogen bonds : bond 0.04661 / 3.11 ( 844) hydrogen bonds : angle 3.39707 / 2.46 ( 2217) metal coordination : bond 0.00481 / 0.19 ( 7) metal coordination : angle 2.54927 / 1.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.570 Fit side-chains REVERT: A 112 ILE cc_start: 0.9557 (OUTLIER) cc_final: 0.9334 (mt) REVERT: B 16 LYS cc_start: 0.4687 (OUTLIER) cc_final: 0.4313 (ptpt) REVERT: D 90 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: W 473 ILE cc_start: 0.3174 (OUTLIER) cc_final: 0.2880 (tp) REVERT: W 560 GLU cc_start: 0.7178 (pp20) cc_final: 0.6903 (pt0) REVERT: W 623 MET cc_start: 0.8069 (ptp) cc_final: 0.7323 (pmm) REVERT: W 981 MET cc_start: 0.8235 (tmm) cc_final: 0.7928 (tmm) REVERT: W 1193 MET cc_start: 0.6624 (mmt) cc_final: 0.5837 (ptt) outliers start: 22 outliers final: 16 residues processed: 156 average time/residue: 0.1448 time to fit residues: 34.3358 Evaluate side-chains 154 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain W residue 473 ILE Chi-restraints excluded: chain W residue 510 TRP Chi-restraints excluded: chain W residue 565 LEU Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 803 VAL Chi-restraints excluded: chain W residue 811 ASP Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 1046 ILE Chi-restraints excluded: chain W residue 1069 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 82 optimal weight: 20.0000 chunk 137 optimal weight: 0.9990 chunk 72 optimal weight: 30.0000 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 153 optimal weight: 0.0770 chunk 36 optimal weight: 0.1980 chunk 19 optimal weight: 5.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 472 HIS W1037 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.140261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106178 restraints weight = 41333.029| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.62 r_work: 0.3196 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18805 Z= 0.137 Angle : 0.597 11.515 26685 Z= 0.340 Chirality : 0.041 0.176 2975 Planarity : 0.005 0.081 2352 Dihedral : 28.156 175.240 4880 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.95 % Allowed : 15.30 % Favored : 82.75 % 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: 0.96 (0.22), residues: 1429 helix: 1.86 (0.19), residues: 798 sheet: -0.48 (0.51), residues: 104 loop : -1.07 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 30 TYR 0.015 0.001 TYR H 39 PHE 0.016 0.001 PHE W 913 TRP 0.009 0.001 TRP W 553 HIS 0.003 0.001 HIS W 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (18798) covalent geometry : angle 0.59589 / 0.34 (26679) hydrogen bonds : bond 0.04542 / 3.04 ( 844) hydrogen bonds : angle 3.33976 / 2.42 ( 2217) metal coordination : bond 0.00430 / 0.19 ( 7) metal coordination : angle 2.26507 / 1.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.608 Fit side-chains REVERT: A 112 ILE cc_start: 0.9549 (OUTLIER) cc_final: 0.9328 (mt) REVERT: B 16 LYS cc_start: 0.4681 (OUTLIER) cc_final: 0.4302 (ptpt) REVERT: D 90 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: W 473 ILE cc_start: 0.3281 (OUTLIER) cc_final: 0.2994 (tp) REVERT: W 560 GLU cc_start: 0.7238 (pp20) cc_final: 0.6967 (pt0) REVERT: W 623 MET cc_start: 0.8067 (ptp) cc_final: 0.7307 (pmm) REVERT: W 1193 MET cc_start: 0.6625 (mmt) cc_final: 0.5829 (ptt) outliers start: 24 outliers final: 17 residues processed: 155 average time/residue: 0.1393 time to fit residues: 33.1423 Evaluate side-chains 157 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain W residue 473 ILE Chi-restraints excluded: chain W residue 510 TRP Chi-restraints excluded: chain W residue 570 MET Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 803 VAL Chi-restraints excluded: chain W residue 809 ASP Chi-restraints excluded: chain W residue 811 ASP Chi-restraints excluded: chain W residue 837 MET Chi-restraints excluded: chain W residue 849 LEU Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 1046 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 131 optimal weight: 0.0050 chunk 47 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 145 optimal weight: 0.7980 chunk 108 optimal weight: 0.2980 chunk 163 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 85 optimal weight: 50.0000 chunk 100 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 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 = 0.3891 r_free = 0.3891 target = 0.140923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106641 restraints weight = 43633.735| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.67 r_work: 0.3213 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18805 Z= 0.124 Angle : 0.586 12.145 26685 Z= 0.336 Chirality : 0.041 0.178 2975 Planarity : 0.004 0.074 2352 Dihedral : 28.097 175.129 4880 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.79 % Allowed : 15.46 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.23), residues: 1429 helix: 1.95 (0.19), residues: 798 sheet: -0.48 (0.51), residues: 104 loop : -0.99 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 30 TYR 0.017 0.001 TYR H 39 PHE 0.018 0.001 PHE W 913 TRP 0.008 0.001 TRP W 736 HIS 0.005 0.001 HIS W 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.12 (18798) covalent geometry : angle 0.58558 / 0.34 (26679) hydrogen bonds : bond 0.04317 / 2.88 ( 844) hydrogen bonds : angle 3.28167 / 2.38 ( 2217) metal coordination : bond 0.00360 / 0.16 ( 7) metal coordination : angle 2.03642 / 1.29 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.606 Fit side-chains REVERT: A 112 ILE cc_start: 0.9550 (OUTLIER) cc_final: 0.9330 (mt) REVERT: B 16 LYS cc_start: 0.4683 (OUTLIER) cc_final: 0.4328 (ptpt) REVERT: D 90 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: W 473 ILE cc_start: 0.3232 (OUTLIER) cc_final: 0.2939 (tp) REVERT: W 560 GLU cc_start: 0.7195 (pp20) cc_final: 0.6990 (pt0) REVERT: W 623 MET cc_start: 0.8064 (ptp) cc_final: 0.7309 (pmm) REVERT: W 981 MET cc_start: 0.8178 (tmm) cc_final: 0.7909 (tmm) REVERT: W 1193 MET cc_start: 0.6613 (mmt) cc_final: 0.5799 (ptt) outliers start: 22 outliers final: 18 residues processed: 156 average time/residue: 0.1440 time to fit residues: 33.9014 Evaluate side-chains 158 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain W residue 473 ILE Chi-restraints excluded: chain W residue 510 TRP Chi-restraints excluded: chain W residue 747 THR Chi-restraints excluded: chain W residue 803 VAL Chi-restraints excluded: chain W residue 809 ASP Chi-restraints excluded: chain W residue 811 ASP Chi-restraints excluded: chain W residue 849 LEU Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 1046 ILE Chi-restraints excluded: chain W residue 1069 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 144 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 135 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 145 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 100 optimal weight: 0.0470 chunk 111 optimal weight: 2.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1037 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.141830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108079 restraints weight = 43941.079| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.62 r_work: 0.3242 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 18805 Z= 0.121 Angle : 0.568 12.282 26685 Z= 0.328 Chirality : 0.040 0.174 2975 Planarity : 0.004 0.062 2352 Dihedral : 28.049 175.190 4880 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.79 % Allowed : 15.70 % Favored : 82.51 % 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: 1.25 (0.23), residues: 1429 helix: 2.06 (0.19), residues: 798 sheet: -0.21 (0.54), residues: 94 loop : -0.89 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 30 TYR 0.012 0.001 TYR D 118 PHE 0.016 0.001 PHE W 913 TRP 0.016 0.001 TRP W 553 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.12 (18798) covalent geometry : angle 0.56736 / 0.33 (26679) hydrogen bonds : bond 0.04109 / 2.75 ( 844) hydrogen bonds : angle 3.19702 / 2.32 ( 2217) metal coordination : bond 0.00313 / 0.14 ( 7) metal coordination : angle 1.91761 / 1.22 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4406.99 seconds wall clock time: 76 minutes 7.43 seconds (4567.43 seconds total)