Starting phenix.real_space_refine on Thu Mar 5 00:36:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ryr_10058/03_2026/6ryr_10058.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ryr_10058/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ryr_10058/03_2026/6ryr_10058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ryr_10058/03_2026/6ryr_10058.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ryr_10058/03_2026/6ryr_10058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ryr_10058/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.00, per 1000 atoms: 0.28 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: 1.68 Conformation dependent library (CDL) restraints added in 792.3 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: 2.85 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: 5.02 Time building geometry restraints manager: 2.22 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=" 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 bond pdb=" O3G ANP W2001 " pdb=" PG ANP W2001 " ideal model delta sigma weight residual 1.528 1.581 -0.053 2.00e-02 2.50e+03 7.09e+00 bond pdb=" O2B ANP W2001 " pdb=" PB ANP W2001 " ideal model delta sigma weight residual 1.508 1.556 -0.048 2.00e-02 2.50e+03 5.71e+00 ... (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=" CB LEU W 480 " pdb=" CG LEU W 480 " pdb=" CD1 LEU W 480 " ideal model delta sigma weight residual 110.70 122.03 -11.33 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O1B ANP W2001 " pdb=" PB ANP W2001 " pdb=" O2B ANP W2001 " ideal model delta sigma weight residual 120.08 109.43 10.65 3.00e+00 1.11e-01 1.26e+01 angle pdb=" CB LEU W 480 " pdb=" CG LEU W 480 " pdb=" CD2 LEU W 480 " ideal model delta sigma weight residual 110.70 120.32 -9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" N3B ANP W2001 " pdb=" PB ANP W2001 " pdb=" O3A ANP W2001 " ideal model delta sigma weight residual 101.56 110.16 -8.60 3.00e+00 1.11e-01 8.22e+00 ... (remaining 26674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 9220 34.91 - 69.82: 1284 69.82 - 104.73: 38 104.73 - 139.64: 0 139.64 - 174.55: 1 Dihedral angle restraints: 10543 sinusoidal: 6280 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 10540 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=" CB ILE W 661 " pdb=" CA ILE W 661 " pdb=" CG1 ILE W 661 " pdb=" CG2 ILE W 661 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.65e-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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.030 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.197 18805 Z= 0.189 Angle : 0.743 43.094 26685 Z= 0.384 Chirality : 0.052 1.773 2975 Planarity : 0.004 0.069 2352 Dihedral : 24.039 174.551 7791 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 covalent geometry : bond 0.00374 (18798) covalent geometry : angle 0.66839 (26679) hydrogen bonds : bond 0.17644 ( 844) hydrogen bonds : angle 5.90608 ( 2217) metal coordination : bond 0.09063 ( 7) metal coordination : angle 21.59820 ( 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 : 0.417 Fit side-chains REVERT: B 16 LYS cc_start: 0.5215 (OUTLIER) cc_final: 0.4691 (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: 0.1845 time to fit residues: 47.4893 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 : 0.524 ------------------------------------------------------------------------------- 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: 8.9990 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: 4.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.5980 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN H 106 HIS W 472 HIS W 573 ASN W 914 HIS W 998 ASN W1037 ASN W1151 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.142101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108355 restraints weight = 40310.831| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.52 r_work: 0.3245 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18805 Z= 0.169 Angle : 0.621 10.234 26685 Z= 0.353 Chirality : 0.039 0.194 2975 Planarity : 0.005 0.071 2352 Dihedral : 27.821 177.882 4908 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.30 % Allowed : 8.14 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.22), residues: 1429 helix: 1.36 (0.19), residues: 796 sheet: -0.38 (0.57), residues: 88 loop : -1.14 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 30 TYR 0.022 0.002 TYR W 574 PHE 0.025 0.002 PHE W 913 TRP 0.016 0.002 TRP W 621 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00378 (18798) covalent geometry : angle 0.61892 (26679) hydrogen bonds : bond 0.04644 ( 844) hydrogen bonds : angle 3.48999 ( 2217) metal coordination : bond 0.00805 ( 7) metal coordination : angle 3.79399 ( 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 175 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.481 Fit side-chains REVERT: B 16 LYS cc_start: 0.4777 (OUTLIER) cc_final: 0.4431 (ptpt) REVERT: G 73 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8233 (t0) REVERT: W 548 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7308 (mt0) REVERT: W 1030 MET cc_start: 0.8376 (tpp) cc_final: 0.8037 (mmp) REVERT: W 1193 MET cc_start: 0.6709 (mmt) cc_final: 0.5825 (ptt) outliers start: 16 outliers final: 4 residues processed: 166 average time/residue: 0.1631 time to fit residues: 39.0808 Evaluate side-chains 145 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 7 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 111 optimal weight: 0.0770 chunk 134 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** H 81 ASN ** 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 = 0.3908 r_free = 0.3908 target = 0.142261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.108028 restraints weight = 44863.985| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.67 r_work: 0.3230 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 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 = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18805 Z= 0.151 Angle : 0.549 8.760 26685 Z= 0.316 Chirality : 0.036 0.173 2975 Planarity : 0.004 0.054 2352 Dihedral : 27.672 175.949 4908 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.30 % Allowed : 10.25 % Favored : 88.45 % 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: 0.85 (0.22), residues: 1429 helix: 1.71 (0.19), residues: 799 sheet: -0.29 (0.56), residues: 94 loop : -1.04 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 30 TYR 0.015 0.001 TYR W 574 PHE 0.021 0.001 PHE W 913 TRP 0.010 0.001 TRP W 621 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00335 (18798) covalent geometry : angle 0.54770 (26679) hydrogen bonds : bond 0.04114 ( 844) hydrogen bonds : angle 3.24749 ( 2217) metal coordination : bond 0.00796 ( 7) metal coordination : angle 2.59989 ( 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 165 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.635 Fit side-chains REVERT: B 16 LYS cc_start: 0.4646 (OUTLIER) cc_final: 0.4327 (ptpt) REVERT: D 56 MET cc_start: 0.8787 (tpt) cc_final: 0.8185 (tpt) REVERT: D 90 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: W 1193 MET cc_start: 0.6597 (mmt) cc_final: 0.5751 (ptt) outliers start: 16 outliers final: 4 residues processed: 155 average time/residue: 0.1567 time to fit residues: 35.9824 Evaluate side-chains 146 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS 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 W residue 510 TRP Chi-restraints excluded: chain W residue 1069 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 114 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN E 39 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 876 HIS W1037 ASN W1155 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.136534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.101619 restraints weight = 39874.804| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.61 r_work: 0.3130 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 18805 Z= 0.321 Angle : 0.666 8.726 26685 Z= 0.373 Chirality : 0.043 0.180 2975 Planarity : 0.006 0.097 2352 Dihedral : 28.420 173.154 4908 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.52 % Allowed : 12.69 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1429 helix: 1.33 (0.18), residues: 796 sheet: -0.51 (0.52), residues: 110 loop : -1.28 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 30 TYR 0.025 0.002 TYR W 712 PHE 0.020 0.002 PHE W 886 TRP 0.016 0.002 TRP W 547 HIS 0.005 0.001 HIS W 474 Details of bonding type rmsd covalent geometry : bond 0.00755 (18798) covalent geometry : angle 0.66290 (26679) hydrogen bonds : bond 0.05562 ( 844) hydrogen bonds : angle 3.60192 ( 2217) metal coordination : bond 0.00773 ( 7) metal coordination : angle 4.21734 ( 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 179 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.540 Fit side-chains REVERT: A 112 ILE cc_start: 0.9587 (OUTLIER) cc_final: 0.9360 (mt) REVERT: B 16 LYS cc_start: 0.4902 (OUTLIER) cc_final: 0.4239 (ptpt) REVERT: D 30 ARG cc_start: 0.7922 (tpp80) cc_final: 0.6809 (tmt170) REVERT: D 56 MET cc_start: 0.8893 (tpt) cc_final: 0.8381 (tpt) REVERT: D 90 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: D 117 LYS cc_start: 0.8991 (ttpt) cc_final: 0.8583 (tttp) REVERT: F 84 MET cc_start: 0.8094 (mmm) cc_final: 0.7800 (mmm) REVERT: H 68 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: W 1193 MET cc_start: 0.6922 (mmt) cc_final: 0.6011 (ptt) outliers start: 31 outliers final: 17 residues processed: 167 average time/residue: 0.1644 time to fit residues: 39.6982 Evaluate side-chains 158 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 ARG 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 E residue 39 HIS 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 747 THR 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 954 MET Chi-restraints excluded: chain W residue 1046 ILE Chi-restraints excluded: chain W residue 1069 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 59 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN E 39 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1037 ASN W1155 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.139037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105111 restraints weight = 47421.053| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.74 r_work: 0.3163 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18805 Z= 0.190 Angle : 0.570 10.294 26685 Z= 0.326 Chirality : 0.037 0.149 2975 Planarity : 0.005 0.070 2352 Dihedral : 28.123 175.778 4908 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.12 % Allowed : 14.32 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.22), residues: 1429 helix: 1.65 (0.18), residues: 799 sheet: -0.51 (0.51), residues: 110 loop : -1.14 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 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 553 HIS 0.010 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00437 (18798) covalent geometry : angle 0.56917 (26679) hydrogen bonds : bond 0.04304 ( 844) hydrogen bonds : angle 3.32880 ( 2217) metal coordination : bond 0.00461 ( 7) metal coordination : angle 2.58288 ( 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 170 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.512 Fit side-chains REVERT: B 16 LYS cc_start: 0.4816 (OUTLIER) cc_final: 0.4259 (ptpt) REVERT: D 30 ARG cc_start: 0.7755 (tpp80) cc_final: 0.6740 (tmt170) REVERT: D 56 MET cc_start: 0.8793 (tpt) cc_final: 0.8271 (tpt) REVERT: D 90 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: D 117 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8480 (tttp) REVERT: E 39 HIS cc_start: 0.6807 (OUTLIER) cc_final: 0.5912 (p-80) REVERT: F 84 MET cc_start: 0.7678 (mmm) cc_final: 0.7466 (mmm) REVERT: H 68 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7266 (mm-30) REVERT: W 1193 MET cc_start: 0.6572 (mmt) cc_final: 0.5893 (ptt) outliers start: 26 outliers final: 15 residues processed: 159 average time/residue: 0.1584 time to fit residues: 37.0859 Evaluate side-chains 156 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 81 ASP 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 E residue 39 HIS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 61 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 449 MET Chi-restraints excluded: chain W residue 510 TRP Chi-restraints excluded: chain W residue 811 ASP Chi-restraints excluded: chain W residue 954 MET Chi-restraints excluded: chain W residue 1046 ILE Chi-restraints excluded: chain W residue 1069 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 120 optimal weight: 0.3980 chunk 164 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 715 GLN W1037 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.141291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108471 restraints weight = 30707.190| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.25 r_work: 0.3274 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18805 Z= 0.141 Angle : 0.532 11.056 26685 Z= 0.306 Chirality : 0.035 0.145 2975 Planarity : 0.004 0.052 2352 Dihedral : 27.940 176.837 4908 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.95 % Allowed : 14.65 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.09 (0.22), residues: 1429 helix: 1.96 (0.19), residues: 800 sheet: -0.34 (0.55), residues: 95 loop : -1.01 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 30 TYR 0.015 0.001 TYR W 712 PHE 0.016 0.001 PHE W 913 TRP 0.009 0.001 TRP W 553 HIS 0.020 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00312 (18798) covalent geometry : angle 0.53075 (26679) hydrogen bonds : bond 0.03699 ( 844) hydrogen bonds : angle 3.13353 ( 2217) metal coordination : bond 0.00284 ( 7) metal coordination : angle 1.99575 ( 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: 24 poor density : 144 time to evaluate : 0.492 Fit side-chains REVERT: A 112 ILE cc_start: 0.9560 (OUTLIER) cc_final: 0.9327 (mt) REVERT: B 16 LYS cc_start: 0.4553 (OUTLIER) cc_final: 0.4166 (ptpt) REVERT: D 30 ARG cc_start: 0.7778 (tpp80) cc_final: 0.6679 (tmt170) REVERT: D 56 MET cc_start: 0.8848 (tpt) cc_final: 0.8513 (mmm) REVERT: D 90 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: D 117 LYS cc_start: 0.8892 (ttpt) cc_final: 0.8510 (tttp) REVERT: H 56 MET cc_start: 0.8822 (tpp) cc_final: 0.8578 (mmt) REVERT: W 1091 TYR cc_start: 0.8354 (m-10) cc_final: 0.8010 (m-10) REVERT: W 1193 MET cc_start: 0.6804 (mmt) cc_final: 0.5914 (ptt) outliers start: 24 outliers final: 14 residues processed: 157 average time/residue: 0.1483 time to fit residues: 34.6743 Evaluate side-chains 154 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS 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 F residue 77 LYS 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 747 THR 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: 3.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.0670 chunk 149 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN E 39 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1037 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.141386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.107733 restraints weight = 42879.934| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.61 r_work: 0.3220 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18805 Z= 0.145 Angle : 0.531 11.237 26685 Z= 0.304 Chirality : 0.035 0.162 2975 Planarity : 0.004 0.043 2352 Dihedral : 27.958 175.052 4908 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.20 % Allowed : 15.22 % Favored : 82.59 % 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: 1.24 (0.23), residues: 1429 helix: 2.07 (0.19), residues: 799 sheet: -0.27 (0.55), residues: 95 loop : -0.92 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 30 TYR 0.016 0.001 TYR D 118 PHE 0.014 0.001 PHE W 913 TRP 0.007 0.001 TRP W 553 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00325 (18798) covalent geometry : angle 0.53043 (26679) hydrogen bonds : bond 0.03739 ( 844) hydrogen bonds : angle 3.12224 ( 2217) metal coordination : bond 0.00291 ( 7) metal coordination : angle 1.79709 ( 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 171 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.554 Fit side-chains REVERT: A 112 ILE cc_start: 0.9541 (OUTLIER) cc_final: 0.9305 (mt) REVERT: B 16 LYS cc_start: 0.5047 (OUTLIER) cc_final: 0.4348 (ptpp) REVERT: D 30 ARG cc_start: 0.7837 (tpp80) cc_final: 0.6724 (tmt170) REVERT: D 56 MET cc_start: 0.8735 (tpt) cc_final: 0.8393 (mmm) REVERT: D 90 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: D 117 LYS cc_start: 0.8833 (ttpt) cc_final: 0.8498 (tttp) REVERT: W 775 LYS cc_start: 0.7429 (ptpt) cc_final: 0.7142 (ptpp) REVERT: W 1091 TYR cc_start: 0.8259 (m-10) cc_final: 0.7924 (m-10) outliers start: 27 outliers final: 16 residues processed: 162 average time/residue: 0.1621 time to fit residues: 38.4083 Evaluate side-chains 162 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS 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 E residue 39 HIS Chi-restraints excluded: chain F residue 77 LYS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 146 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 134 optimal weight: 0.0670 chunk 157 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 142 optimal weight: 30.0000 chunk 31 optimal weight: 0.8980 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 448 HIS W1037 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.141490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.107932 restraints weight = 44285.360| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.70 r_work: 0.3219 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18805 Z= 0.142 Angle : 0.524 11.737 26685 Z= 0.300 Chirality : 0.034 0.149 2975 Planarity : 0.004 0.042 2352 Dihedral : 27.916 175.287 4908 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.87 % Allowed : 15.62 % 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: 1.30 (0.23), residues: 1429 helix: 2.11 (0.19), residues: 799 sheet: -0.21 (0.55), residues: 95 loop : -0.89 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 30 TYR 0.014 0.001 TYR H 39 PHE 0.014 0.001 PHE W 913 TRP 0.009 0.001 TRP W 553 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00318 (18798) covalent geometry : angle 0.52337 (26679) hydrogen bonds : bond 0.03649 ( 844) hydrogen bonds : angle 3.08315 ( 2217) metal coordination : bond 0.00266 ( 7) metal coordination : angle 1.84780 ( 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 166 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.550 Fit side-chains REVERT: A 112 ILE cc_start: 0.9536 (OUTLIER) cc_final: 0.9297 (mt) REVERT: B 16 LYS cc_start: 0.5046 (OUTLIER) cc_final: 0.4271 (ptpp) REVERT: D 30 ARG cc_start: 0.7817 (tpp80) cc_final: 0.6721 (tmt170) REVERT: D 56 MET cc_start: 0.8731 (tpt) cc_final: 0.8389 (mmm) REVERT: D 90 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: W 608 MET cc_start: 0.7911 (tpp) cc_final: 0.7655 (mmt) REVERT: W 775 LYS cc_start: 0.7479 (ptpt) cc_final: 0.7189 (ptpp) REVERT: W 1091 TYR cc_start: 0.8263 (m-10) cc_final: 0.7925 (m-10) outliers start: 23 outliers final: 17 residues processed: 158 average time/residue: 0.1547 time to fit residues: 36.4511 Evaluate side-chains 159 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS 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 F residue 77 LYS Chi-restraints excluded: chain G residue 61 GLU 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 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 Chi-restraints excluded: chain W residue 1123 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 82 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3875 r_free = 0.3875 target = 0.139440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.105849 restraints weight = 39954.269| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.51 r_work: 0.3194 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18805 Z= 0.187 Angle : 0.557 11.329 26685 Z= 0.316 Chirality : 0.036 0.162 2975 Planarity : 0.004 0.041 2352 Dihedral : 28.163 174.800 4908 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.79 % Allowed : 16.11 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.22), residues: 1429 helix: 1.96 (0.19), residues: 800 sheet: -0.16 (0.56), residues: 95 loop : -0.95 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 42 TYR 0.017 0.001 TYR D 118 PHE 0.014 0.002 PHE W 886 TRP 0.006 0.001 TRP W 488 HIS 0.007 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00431 (18798) covalent geometry : angle 0.55652 (26679) hydrogen bonds : bond 0.04236 ( 844) hydrogen bonds : angle 3.23783 ( 2217) metal coordination : bond 0.00377 ( 7) metal coordination : angle 2.20862 ( 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 162 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.536 Fit side-chains REVERT: A 112 ILE cc_start: 0.9584 (OUTLIER) cc_final: 0.9334 (mt) REVERT: B 16 LYS cc_start: 0.4956 (OUTLIER) cc_final: 0.3988 (mtmm) REVERT: D 30 ARG cc_start: 0.7903 (tpp80) cc_final: 0.6853 (tmt170) REVERT: D 56 MET cc_start: 0.8859 (tpt) cc_final: 0.8334 (tpt) REVERT: D 90 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: W 608 MET cc_start: 0.7851 (tpp) cc_final: 0.7574 (mmt) REVERT: W 623 MET cc_start: 0.8035 (pmm) cc_final: 0.7471 (pmm) REVERT: W 775 LYS cc_start: 0.7570 (ptpt) cc_final: 0.7289 (ptpp) REVERT: W 1091 TYR cc_start: 0.8430 (m-10) cc_final: 0.8053 (m-10) REVERT: W 1193 MET cc_start: 0.6815 (mmt) cc_final: 0.5968 (ptt) outliers start: 22 outliers final: 17 residues processed: 156 average time/residue: 0.1544 time to fit residues: 35.6547 Evaluate side-chains 159 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS 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 C residue 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 61 GLU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 131 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 123 optimal weight: 0.1980 chunk 113 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 10.9990 chunk 100 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3876 r_free = 0.3876 target = 0.139624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.105608 restraints weight = 41586.215| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.59 r_work: 0.3193 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- 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 = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18805 Z= 0.139 Angle : 0.550 11.781 26685 Z= 0.313 Chirality : 0.035 0.175 2975 Planarity : 0.004 0.047 2352 Dihedral : 28.134 175.094 4908 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.55 % Allowed : 16.35 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.23), residues: 1429 helix: 2.02 (0.19), residues: 800 sheet: -0.17 (0.56), residues: 95 loop : -0.92 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 572 TYR 0.024 0.001 TYR F 88 PHE 0.015 0.001 PHE W 913 TRP 0.008 0.001 TRP W 553 HIS 0.007 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00308 (18798) covalent geometry : angle 0.54961 (26679) hydrogen bonds : bond 0.03971 ( 844) hydrogen bonds : angle 3.23098 ( 2217) metal coordination : bond 0.00301 ( 7) metal coordination : angle 2.00935 ( 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 155 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.557 Fit side-chains REVERT: A 112 ILE cc_start: 0.9545 (OUTLIER) cc_final: 0.9303 (mt) REVERT: B 16 LYS cc_start: 0.5293 (OUTLIER) cc_final: 0.4269 (mtmm) REVERT: D 30 ARG cc_start: 0.7791 (tpp80) cc_final: 0.6851 (tmt170) REVERT: D 56 MET cc_start: 0.8727 (tpt) cc_final: 0.8226 (tpt) REVERT: D 90 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: W 608 MET cc_start: 0.7905 (tpp) cc_final: 0.7625 (mmt) REVERT: W 623 MET cc_start: 0.7880 (pmm) cc_final: 0.7286 (pmm) REVERT: W 775 LYS cc_start: 0.7390 (ptpt) cc_final: 0.7133 (ptpp) outliers start: 19 outliers final: 15 residues processed: 150 average time/residue: 0.1552 time to fit residues: 34.3294 Evaluate side-chains 151 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS 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 F residue 77 LYS Chi-restraints excluded: chain G residue 61 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 144 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 62 optimal weight: 0.0670 chunk 135 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 145 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3880 r_free = 0.3880 target = 0.139893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.105525 restraints weight = 42636.285| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.67 r_work: 0.3183 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3265 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= 0.144 Angle : 0.544 12.054 26685 Z= 0.309 Chirality : 0.035 0.152 2975 Planarity : 0.004 0.047 2352 Dihedral : 28.069 174.937 4908 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.63 % Allowed : 16.19 % Favored : 82.18 % 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: 1.23 (0.23), residues: 1429 helix: 2.05 (0.19), residues: 799 sheet: -0.18 (0.56), residues: 95 loop : -0.92 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 71 TYR 0.014 0.001 TYR D 118 PHE 0.015 0.001 PHE W 913 TRP 0.015 0.001 TRP W 553 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00320 (18798) covalent geometry : angle 0.54386 (26679) hydrogen bonds : bond 0.03854 ( 844) hydrogen bonds : angle 3.18479 ( 2217) metal coordination : bond 0.00293 ( 7) metal coordination : angle 1.82385 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4593.57 seconds wall clock time: 79 minutes 7.29 seconds (4747.29 seconds total)