Starting phenix.real_space_refine on Fri Jul 3 19:12:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qxa_14196/07_2026/7qxa_14196_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qxa_14196/07_2026/7qxa_14196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qxa_14196/07_2026/7qxa_14196_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qxa_14196/07_2026/7qxa_14196_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qxa_14196/07_2026/7qxa_14196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qxa_14196/07_2026/7qxa_14196.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 265 5.49 5 S 42 5.16 5 C 8869 2.51 5 N 2831 2.21 5 O 3569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15576 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 7649 Classifications: {'peptide': 954} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 55, 'TRANS': 895} Chain breaks: 3 Chain: "B" Number of atoms: 5371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 5371 Classifications: {'RNA': 253} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 19, 'rna3p_pur': 99, 'rna3p_pyr': 118} Link IDs: {'rna2p': 36, 'rna3p': 216} Chain breaks: 3 Chain: "L" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 632 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "M" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "N" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 254 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "O" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain breaks: 3 Time building chain proxies: 3.32, per 1000 atoms: 0.21 Number of scatterers: 15576 At special positions: 0 Unit cell: (166.77, 123.17, 146.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 265 15.00 O 3569 8.00 N 2831 7.00 C 8869 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: 1.21 Conformation dependent library (CDL) restraints added in 478.3 milliseconds 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2346 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 9 sheets defined 54.3% alpha, 12.7% beta 51 base pairs and 131 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 removed outlier: 3.910A pdb=" N ARG A 11 " --> pdb=" O CYS A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 44 through 53 removed outlier: 3.582A pdb=" N VAL A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 92 removed outlier: 3.583A pdb=" N VAL A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 removed outlier: 3.863A pdb=" N GLY A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.799A pdb=" N ARG A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.725A pdb=" N LEU A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 353 through 366 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 389 through 402 removed outlier: 3.657A pdb=" N PHE A 393 " --> pdb=" O MET A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.503A pdb=" N LEU A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 454 removed outlier: 3.537A pdb=" N ARG A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 473 removed outlier: 3.938A pdb=" N ARG A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.691A pdb=" N TRP A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 497 removed outlier: 3.545A pdb=" N LYS A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 496 " --> pdb=" O LYS A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.679A pdb=" N LEU A 520 " --> pdb=" O CYS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 551 removed outlier: 3.542A pdb=" N LYS A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 removed outlier: 3.655A pdb=" N PHE A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 597 removed outlier: 3.741A pdb=" N LYS A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 596 " --> pdb=" O HIS A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.681A pdb=" N GLU A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 672 removed outlier: 4.112A pdb=" N LYS A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 676 Processing helix chain 'A' and resid 682 through 698 removed outlier: 3.869A pdb=" N THR A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 734 removed outlier: 3.659A pdb=" N GLU A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 733 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 769 removed outlier: 3.570A pdb=" N LEU A 769 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 784 Processing helix chain 'A' and resid 802 through 814 Processing helix chain 'A' and resid 837 through 854 removed outlier: 3.669A pdb=" N CYS A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A 843 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 859 Processing helix chain 'A' and resid 876 through 890 removed outlier: 3.675A pdb=" N ALA A 880 " --> pdb=" O HIS A 876 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 890 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 950 removed outlier: 3.646A pdb=" N TYR A 949 " --> pdb=" O TYR A 946 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 950 " --> pdb=" O SER A 947 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 946 through 950' Processing helix chain 'A' and resid 965 through 982 removed outlier: 3.588A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 993 through 1017 removed outlier: 3.604A pdb=" N LEU A1007 " --> pdb=" O LYS A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1028 removed outlier: 3.554A pdb=" N LYS A1027 " --> pdb=" O GLN A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1051 removed outlier: 3.588A pdb=" N ASP A1038 " --> pdb=" O ARG A1034 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS A1043 " --> pdb=" O THR A1039 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1085 removed outlier: 3.897A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS A1075 " --> pdb=" O GLN A1071 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR A1083 " --> pdb=" O LEU A1079 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.579A pdb=" N TYR A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) Proline residue: A1091 - end of helix removed outlier: 4.073A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A1102 " --> pdb=" O THR A1098 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A1106 " --> pdb=" O GLN A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1119 removed outlier: 3.894A pdb=" N THR A1113 " --> pdb=" O GLY A1109 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 38 removed outlier: 4.389A pdb=" N LEU L 34 " --> pdb=" O ARG L 30 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU L 35 " --> pdb=" O VAL L 31 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY L 38 " --> pdb=" O LEU L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 73 removed outlier: 4.489A pdb=" N VAL L 50 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR L 51 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU L 56 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU L 57 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU L 66 " --> pdb=" O GLU L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 91 removed outlier: 3.964A pdb=" N LEU L 84 " --> pdb=" O ILE L 80 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG L 89 " --> pdb=" O GLN L 85 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP L 91 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 99 removed outlier: 3.639A pdb=" N ASN L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS L 96 " --> pdb=" O GLU L 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 50 removed outlier: 3.662A pdb=" N VAL M 45 " --> pdb=" O TYR M 41 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS M 47 " --> pdb=" O TYR M 43 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN M 48 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL M 49 " --> pdb=" O VAL M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 86 removed outlier: 3.995A pdb=" N SER M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE M 66 " --> pdb=" O ILE M 62 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE M 70 " --> pdb=" O PHE M 66 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS M 83 " --> pdb=" O SER M 79 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR M 84 " --> pdb=" O ARG M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 103 removed outlier: 3.769A pdb=" N ILE M 95 " --> pdb=" O THR M 91 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN M 96 " --> pdb=" O SER M 92 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N THR M 97 " --> pdb=" O ARG M 93 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG M 100 " --> pdb=" O GLN M 96 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU M 103 " --> pdb=" O VAL M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 125 removed outlier: 3.747A pdb=" N SER M 113 " --> pdb=" O LYS M 109 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU M 114 " --> pdb=" O HIS M 110 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY M 115 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR M 120 " --> pdb=" O THR M 116 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER M 125 " --> pdb=" O LYS M 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 104 removed outlier: 3.837A pdb=" N ILE O 103 " --> pdb=" O ILE O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 164 removed outlier: 3.623A pdb=" N LEU O 162 " --> pdb=" O THR O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 238 removed outlier: 3.527A pdb=" N LYS O 232 " --> pdb=" O LEU O 228 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS O 233 " --> pdb=" O ASP O 229 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR O 235 " --> pdb=" O GLN O 231 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP O 236 " --> pdb=" O LYS O 232 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS O 237 " --> pdb=" O LYS O 233 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU O 238 " --> pdb=" O LEU O 234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23 removed outlier: 3.778A pdb=" N ALA A 157 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 11.317A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER A 796 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 741 " --> pdb=" O SER A 796 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23 removed outlier: 3.778A pdb=" N ALA A 157 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 11.317A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER A 796 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 741 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 739 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 564 Processing sheet with id=AA6, first strand: chain 'A' and resid 599 through 600 removed outlier: 7.356A pdb=" N LEU A 617 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ARG A 819 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N SER A 619 " --> pdb=" O ARG A 819 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 679 through 680 removed outlier: 3.720A pdb=" N LEU A 866 " --> pdb=" O ASP A 869 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 869 " --> pdb=" O LEU A 866 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 711 " --> pdb=" O PHE A 870 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 709 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 905 " --> pdb=" O VAL A 920 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 927 through 930 Processing sheet with id=AA9, first strand: chain 'O' and resid 181 through 184 removed outlier: 7.223A pdb=" N LEU O 145 " --> pdb=" O LEU O 118 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL O 120 " --> pdb=" O THR O 143 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N THR O 143 " --> pdb=" O VAL O 120 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N LEU O 204 " --> pdb=" O SER O 152 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ARG O 154 " --> pdb=" O LEU O 204 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL O 206 " --> pdb=" O ARG O 154 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU O 156 " --> pdb=" O VAL O 206 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1311 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 135 hydrogen bonds 258 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 131 stacking parallelities Total time for adding SS restraints: 3.73 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2427 1.33 - 1.46: 6059 1.46 - 1.59: 7519 1.59 - 1.73: 381 1.73 - 1.86: 55 Bond restraints: 16441 Sorted by residual: bond pdb=" O3' A B 176 " pdb=" P U B 177 " ideal model delta sigma weight residual 1.607 1.697 -0.090 1.50e-02 4.44e+03 3.56e+01 bond pdb=" CA ILE A 624 " pdb=" C ILE A 624 " ideal model delta sigma weight residual 1.524 1.585 -0.060 1.05e-02 9.07e+03 3.31e+01 bond pdb=" C SER A 513 " pdb=" O SER A 513 " ideal model delta sigma weight residual 1.234 1.303 -0.069 1.23e-02 6.61e+03 3.13e+01 bond pdb=" CA PHE A1031 " pdb=" C PHE A1031 " ideal model delta sigma weight residual 1.524 1.467 0.057 1.32e-02 5.74e+03 1.87e+01 bond pdb=" CA SER A 513 " pdb=" C SER A 513 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.30e-02 5.92e+03 1.72e+01 ... (remaining 16436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 20964 1.89 - 3.78: 2307 3.78 - 5.67: 211 5.67 - 7.56: 38 7.56 - 9.44: 9 Bond angle restraints: 23529 Sorted by residual: angle pdb=" O3' C B 72 " pdb=" C3' C B 72 " pdb=" C2' C B 72 " ideal model delta sigma weight residual 109.50 118.94 -9.44 1.50e+00 4.44e-01 3.96e+01 angle pdb=" O3' G B 44 " pdb=" C3' G B 44 " pdb=" C2' G B 44 " ideal model delta sigma weight residual 113.70 122.65 -8.95 1.50e+00 4.44e-01 3.56e+01 angle pdb=" C4' C B 74 " pdb=" C3' C B 74 " pdb=" O3' C B 74 " ideal model delta sigma weight residual 109.40 118.02 -8.62 1.50e+00 4.44e-01 3.31e+01 angle pdb=" N SER A 838 " pdb=" CA SER A 838 " pdb=" C SER A 838 " ideal model delta sigma weight residual 111.33 117.93 -6.60 1.21e+00 6.83e-01 2.98e+01 angle pdb=" O3' A B 174 " pdb=" C3' A B 174 " pdb=" C2' A B 174 " ideal model delta sigma weight residual 113.70 121.73 -8.03 1.50e+00 4.44e-01 2.87e+01 ... (remaining 23524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 9513 35.95 - 71.89: 700 71.89 - 107.84: 107 107.84 - 143.78: 8 143.78 - 179.73: 10 Dihedral angle restraints: 10338 sinusoidal: 6717 harmonic: 3621 Sorted by residual: dihedral pdb=" C5' C B 74 " pdb=" C4' C B 74 " pdb=" C3' C B 74 " pdb=" O3' C B 74 " ideal model delta sinusoidal sigma weight residual 147.00 74.89 72.11 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" C4' C B 74 " pdb=" C3' C B 74 " pdb=" C2' C B 74 " pdb=" C1' C B 74 " ideal model delta sinusoidal sigma weight residual -35.00 33.16 -68.16 1 8.00e+00 1.56e-02 9.42e+01 dihedral pdb=" C5' A B 176 " pdb=" C4' A B 176 " pdb=" C3' A B 176 " pdb=" O3' A B 176 " ideal model delta sinusoidal sigma weight residual 147.00 79.66 67.34 1 8.00e+00 1.56e-02 9.22e+01 ... (remaining 10335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2201 0.101 - 0.203: 552 0.203 - 0.304: 107 0.304 - 0.405: 6 0.405 - 0.506: 4 Chirality restraints: 2870 Sorted by residual: chirality pdb=" C3' C B 72 " pdb=" C4' C B 72 " pdb=" O3' C B 72 " pdb=" C2' C B 72 " both_signs ideal model delta sigma weight residual False -2.74 -2.24 -0.51 2.00e-01 2.50e+01 6.41e+00 chirality pdb=" C3' G B 300 " pdb=" C4' G B 300 " pdb=" O3' G B 300 " pdb=" C2' G B 300 " both_signs ideal model delta sigma weight residual False -2.74 -2.24 -0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" C3' U B 42 " pdb=" C4' U B 42 " pdb=" O3' U B 42 " pdb=" C2' U B 42 " both_signs ideal model delta sigma weight residual False -2.74 -2.26 -0.49 2.00e-01 2.50e+01 5.90e+00 ... (remaining 2867 not shown) Planarity restraints: 2018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 177 " -0.104 2.00e-02 2.50e+03 5.14e-02 5.95e+01 pdb=" N1 U B 177 " 0.057 2.00e-02 2.50e+03 pdb=" C2 U B 177 " 0.041 2.00e-02 2.50e+03 pdb=" O2 U B 177 " 0.037 2.00e-02 2.50e+03 pdb=" N3 U B 177 " -0.047 2.00e-02 2.50e+03 pdb=" C4 U B 177 " -0.040 2.00e-02 2.50e+03 pdb=" O4 U B 177 " -0.009 2.00e-02 2.50e+03 pdb=" C5 U B 177 " 0.011 2.00e-02 2.50e+03 pdb=" C6 U B 177 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 307 " -0.068 2.00e-02 2.50e+03 3.50e-02 2.75e+01 pdb=" N1 U B 307 " 0.061 2.00e-02 2.50e+03 pdb=" C2 U B 307 " 0.014 2.00e-02 2.50e+03 pdb=" O2 U B 307 " 0.010 2.00e-02 2.50e+03 pdb=" N3 U B 307 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U B 307 " -0.040 2.00e-02 2.50e+03 pdb=" O4 U B 307 " -0.012 2.00e-02 2.50e+03 pdb=" C5 U B 307 " 0.021 2.00e-02 2.50e+03 pdb=" C6 U B 307 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 30 " -0.036 2.00e-02 2.50e+03 2.63e-02 2.08e+01 pdb=" N9 DG N 30 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DG N 30 " 0.021 2.00e-02 2.50e+03 pdb=" N7 DG N 30 " 0.030 2.00e-02 2.50e+03 pdb=" C5 DG N 30 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DG N 30 " -0.023 2.00e-02 2.50e+03 pdb=" O6 DG N 30 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DG N 30 " -0.032 2.00e-02 2.50e+03 pdb=" C2 DG N 30 " -0.003 2.00e-02 2.50e+03 pdb=" N2 DG N 30 " 0.054 2.00e-02 2.50e+03 pdb=" N3 DG N 30 " -0.019 2.00e-02 2.50e+03 pdb=" C4 DG N 30 " -0.015 2.00e-02 2.50e+03 ... (remaining 2015 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1975 2.78 - 3.31: 13932 3.31 - 3.84: 25459 3.84 - 4.37: 30664 4.37 - 4.90: 47163 Nonbonded interactions: 119193 Sorted by model distance: nonbonded pdb=" OP1 C B 320 " pdb=" OH TYR M 41 " model vdw 2.254 3.040 nonbonded pdb=" NH2 ARG A 535 " pdb=" O2' A B 302 " model vdw 2.276 3.120 nonbonded pdb=" O4' U B 316 " pdb=" O2 U B 316 " model vdw 2.303 3.040 nonbonded pdb=" O TRP A 510 " pdb=" O2' C B 313 " model vdw 2.304 3.040 nonbonded pdb=" O4' U B 194 " pdb=" O2 U B 194 " model vdw 2.366 3.040 ... (remaining 119188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 17.290 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 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 : 0.010 0.090 16441 Z= 0.649 Angle : 1.183 9.445 23529 Z= 0.785 Chirality : 0.092 0.506 2870 Planarity : 0.006 0.051 2018 Dihedral : 22.115 179.730 7992 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.03 % Favored : 93.56 % Rotamer: Outliers : 0.28 % Allowed : 2.05 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -3.16 (0.19), residues: 1227 helix: -2.02 (0.17), residues: 538 sheet: -2.06 (0.43), residues: 96 loop : -2.10 (0.22), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 669 TYR 0.043 0.006 TYR A 949 PHE 0.030 0.005 PHE A 870 TRP 0.026 0.005 TRP A 547 HIS 0.014 0.003 HIS A1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00973 / 0.65 (16441) covalent geometry : angle 1.18252 / 0.78 (23529) hydrogen bonds : bond 0.29839 / 20.33 ( 575) hydrogen bonds : angle 8.54143 / 6.14 ( 1569) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 158 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8261 (mp0) REVERT: A 86 GLN cc_start: 0.7885 (tt0) cc_final: 0.7432 (tp-100) REVERT: A 95 ASN cc_start: 0.7957 (t0) cc_final: 0.7515 (t0) REVERT: A 99 PHE cc_start: 0.6908 (m-10) cc_final: 0.6657 (m-80) REVERT: A 142 ARG cc_start: 0.7195 (mtp180) cc_final: 0.6457 (tpt90) REVERT: A 159 PHE cc_start: 0.7091 (m-80) cc_final: 0.6633 (m-80) REVERT: A 603 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8410 (tm-30) REVERT: A 636 MET cc_start: 0.8316 (mmt) cc_final: 0.8095 (mmt) REVERT: A 743 ARG cc_start: 0.6819 (mtt90) cc_final: 0.6568 (mtp85) REVERT: A 756 ARG cc_start: 0.6205 (mtp-110) cc_final: 0.5476 (mmt180) REVERT: A 800 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6871 (mm-30) REVERT: A 889 ARG cc_start: 0.9026 (ttt-90) cc_final: 0.8516 (ptp-170) REVERT: A 899 ASN cc_start: 0.8230 (t0) cc_final: 0.7853 (t0) REVERT: A 922 MET cc_start: 0.7350 (mmm) cc_final: 0.7139 (mtp) REVERT: L 69 ASN cc_start: 0.6793 (t0) cc_final: 0.6586 (m-40) REVERT: M 63 MET cc_start: 0.7274 (mtt) cc_final: 0.6764 (mmp) REVERT: M 117 LYS cc_start: 0.6361 (mttt) cc_final: 0.6006 (mtpt) REVERT: O 165 SER cc_start: 0.4853 (t) cc_final: 0.4564 (m) REVERT: O 170 LYS cc_start: 0.7804 (ptpt) cc_final: 0.7049 (tppt) REVERT: O 175 ARG cc_start: 0.7238 (mtt-85) cc_final: 0.6621 (mtt180) REVERT: O 205 GLN cc_start: 0.8061 (tt0) cc_final: 0.7779 (pp30) REVERT: O 209 PHE cc_start: 0.7767 (p90) cc_final: 0.7345 (p90) REVERT: O 219 LEU cc_start: 0.7588 (mt) cc_final: 0.7382 (tp) outliers start: 3 outliers final: 0 residues processed: 160 average time/residue: 0.1712 time to fit residues: 37.3104 Evaluate side-chains 91 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 HIS A 460 GLN A1013 HIS L 74 ASN L 90 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.145876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.095013 restraints weight = 37213.877| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.22 r_work: 0.3340 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16441 Z= 0.170 Angle : 0.665 9.729 23529 Z= 0.383 Chirality : 0.042 0.308 2870 Planarity : 0.005 0.059 2018 Dihedral : 23.952 175.032 5573 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.42 % Favored : 96.50 % Rotamer: Outliers : 0.74 % Allowed : 7.73 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.47 (0.21), residues: 1227 helix: -0.05 (0.20), residues: 569 sheet: -1.80 (0.41), residues: 120 loop : -1.74 (0.23), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 208 TYR 0.014 0.002 TYR A 176 PHE 0.020 0.002 PHE A 331 TRP 0.018 0.002 TRP A 547 HIS 0.006 0.001 HIS L 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (16441) covalent geometry : angle 0.66466 / 0.38 (23529) hydrogen bonds : bond 0.07671 / 5.21 ( 575) hydrogen bonds : angle 4.96898 / 3.60 ( 1569) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8240 (mp0) REVERT: A 95 ASN cc_start: 0.7921 (t0) cc_final: 0.7433 (t0) REVERT: A 99 PHE cc_start: 0.7961 (m-10) cc_final: 0.7627 (m-80) REVERT: A 139 LEU cc_start: 0.6053 (tp) cc_final: 0.5356 (mp) REVERT: A 159 PHE cc_start: 0.7330 (m-80) cc_final: 0.6872 (m-80) REVERT: L 32 ARG cc_start: 0.6116 (mtp180) cc_final: 0.5680 (ttt-90) REVERT: L 86 LEU cc_start: 0.7298 (mt) cc_final: 0.7056 (tp) REVERT: M 63 MET cc_start: 0.6956 (mtt) cc_final: 0.6702 (mmp) REVERT: M 117 LYS cc_start: 0.6674 (mttt) cc_final: 0.6294 (mtpt) REVERT: O 99 ILE cc_start: 0.7995 (mt) cc_final: 0.7783 (mm) REVERT: O 100 ARG cc_start: 0.7243 (ttp-170) cc_final: 0.7021 (ttp-170) REVERT: O 170 LYS cc_start: 0.8129 (ptpt) cc_final: 0.7425 (tppt) REVERT: O 175 ARG cc_start: 0.6928 (mtt-85) cc_final: 0.6491 (mtt180) REVERT: O 186 ASP cc_start: 0.8406 (t70) cc_final: 0.8132 (t70) outliers start: 8 outliers final: 4 residues processed: 112 average time/residue: 0.1605 time to fit residues: 25.1383 Evaluate side-chains 96 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 719 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 18 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 110 optimal weight: 50.0000 chunk 67 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 138 optimal weight: 0.2980 chunk 16 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 794 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.146069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.095660 restraints weight = 37683.441| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.22 r_work: 0.3354 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16441 Z= 0.128 Angle : 0.553 8.471 23529 Z= 0.317 Chirality : 0.038 0.277 2870 Planarity : 0.005 0.049 2018 Dihedral : 23.574 170.896 5573 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.09 % Rotamer: Outliers : 1.21 % Allowed : 8.47 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.23), residues: 1227 helix: 0.67 (0.21), residues: 579 sheet: -1.23 (0.43), residues: 129 loop : -1.49 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 218 TYR 0.015 0.001 TYR A 772 PHE 0.014 0.001 PHE A 331 TRP 0.015 0.001 TRP A 547 HIS 0.005 0.001 HIS L 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (16441) covalent geometry : angle 0.55339 / 0.32 (23529) hydrogen bonds : bond 0.06080 / 4.19 ( 575) hydrogen bonds : angle 4.38407 / 3.19 ( 1569) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ASN cc_start: 0.7988 (t0) cc_final: 0.7474 (t0) REVERT: A 99 PHE cc_start: 0.8021 (m-10) cc_final: 0.7676 (m-80) REVERT: A 139 LEU cc_start: 0.5597 (tp) cc_final: 0.5310 (mp) REVERT: A 159 PHE cc_start: 0.7345 (m-80) cc_final: 0.6747 (m-80) REVERT: A 901 ARG cc_start: 0.8252 (mmt180) cc_final: 0.7975 (mpt180) REVERT: A 1017 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8642 (mp) REVERT: L 32 ARG cc_start: 0.6162 (mtp180) cc_final: 0.5675 (ttt-90) REVERT: L 64 LEU cc_start: 0.5516 (tp) cc_final: 0.5164 (tp) REVERT: L 74 ASN cc_start: 0.6532 (t0) cc_final: 0.6301 (t0) REVERT: L 86 LEU cc_start: 0.7070 (mt) cc_final: 0.6864 (tp) REVERT: M 117 LYS cc_start: 0.6649 (mttt) cc_final: 0.6250 (mtpt) REVERT: O 99 ILE cc_start: 0.7982 (mt) cc_final: 0.7651 (mm) REVERT: O 100 ARG cc_start: 0.7303 (ttp-170) cc_final: 0.7073 (ttp-170) REVERT: O 170 LYS cc_start: 0.8113 (ptpt) cc_final: 0.7275 (tppt) REVERT: O 175 ARG cc_start: 0.6904 (mtt-85) cc_final: 0.6514 (mtt180) REVERT: O 187 CYS cc_start: 0.7967 (p) cc_final: 0.7606 (p) outliers start: 13 outliers final: 7 residues processed: 112 average time/residue: 0.1454 time to fit residues: 23.4170 Evaluate side-chains 98 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain L residue 24 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 899 ASN ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 ASN M 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.143706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.092487 restraints weight = 37164.747| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.23 r_work: 0.3297 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16441 Z= 0.194 Angle : 0.628 10.301 23529 Z= 0.348 Chirality : 0.040 0.283 2870 Planarity : 0.006 0.061 2018 Dihedral : 23.566 167.243 5573 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.16 % Favored : 95.76 % Rotamer: Outliers : 2.05 % Allowed : 9.12 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.60 (0.23), residues: 1227 helix: 0.65 (0.21), residues: 577 sheet: -0.97 (0.43), residues: 129 loop : -1.41 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 100 TYR 0.012 0.002 TYR A 638 PHE 0.022 0.002 PHE A 331 TRP 0.014 0.002 TRP A 547 HIS 0.009 0.002 HIS A1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (16441) covalent geometry : angle 0.62803 / 0.35 (23529) hydrogen bonds : bond 0.06681 / 4.58 ( 575) hydrogen bonds : angle 4.44975 / 3.21 ( 1569) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ASN cc_start: 0.7965 (t0) cc_final: 0.7472 (t0) REVERT: A 139 LEU cc_start: 0.5807 (tp) cc_final: 0.5443 (mp) REVERT: A 159 PHE cc_start: 0.7325 (m-80) cc_final: 0.6705 (m-80) REVERT: A 1017 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8936 (mp) REVERT: L 32 ARG cc_start: 0.6216 (mtp180) cc_final: 0.5716 (ttt-90) REVERT: L 74 ASN cc_start: 0.6641 (OUTLIER) cc_final: 0.6380 (t0) REVERT: L 86 LEU cc_start: 0.7214 (mt) cc_final: 0.6920 (tp) REVERT: M 117 LYS cc_start: 0.6643 (mttt) cc_final: 0.6284 (mtpt) REVERT: O 169 GLU cc_start: 0.7104 (pm20) cc_final: 0.6770 (pm20) REVERT: O 170 LYS cc_start: 0.8094 (ptpt) cc_final: 0.7270 (tppt) REVERT: O 175 ARG cc_start: 0.7265 (mtt-85) cc_final: 0.6888 (mtt180) outliers start: 22 outliers final: 17 residues processed: 98 average time/residue: 0.1446 time to fit residues: 20.5273 Evaluate side-chains 103 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 74 ASN Chi-restraints excluded: chain O residue 174 PHE Chi-restraints excluded: chain O residue 183 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 30.0000 chunk 117 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 39 optimal weight: 0.0870 chunk 130 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 chunk 133 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 GLN M 50 HIS O 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.144454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.096087 restraints weight = 37305.082| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.30 r_work: 0.3307 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16441 Z= 0.141 Angle : 0.549 10.128 23529 Z= 0.309 Chirality : 0.037 0.280 2870 Planarity : 0.005 0.065 2018 Dihedral : 23.548 168.905 5573 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.09 % Rotamer: Outliers : 1.96 % Allowed : 10.15 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.35 (0.23), residues: 1227 helix: 0.82 (0.21), residues: 584 sheet: -0.81 (0.44), residues: 129 loop : -1.27 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 82 TYR 0.012 0.001 TYR A 894 PHE 0.015 0.001 PHE A 331 TRP 0.013 0.001 TRP A 547 HIS 0.005 0.001 HIS A1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (16441) covalent geometry : angle 0.54910 / 0.31 (23529) hydrogen bonds : bond 0.05598 / 3.81 ( 575) hydrogen bonds : angle 4.19242 / 3.03 ( 1569) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8194 (mm-30) REVERT: A 95 ASN cc_start: 0.8174 (t0) cc_final: 0.7664 (t0) REVERT: A 139 LEU cc_start: 0.5776 (tp) cc_final: 0.5409 (mp) REVERT: A 159 PHE cc_start: 0.7166 (m-80) cc_final: 0.6836 (m-80) REVERT: A 866 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8242 (tp) REVERT: A 894 TYR cc_start: 0.7828 (m-80) cc_final: 0.7613 (m-10) REVERT: A 970 MET cc_start: 0.8572 (ttm) cc_final: 0.8362 (ttt) REVERT: L 32 ARG cc_start: 0.6214 (mtp180) cc_final: 0.5646 (ttt-90) REVERT: L 86 LEU cc_start: 0.7058 (mt) cc_final: 0.6777 (tp) REVERT: M 117 LYS cc_start: 0.6497 (mttt) cc_final: 0.6191 (mtpt) REVERT: O 96 ARG cc_start: 0.7735 (mmm-85) cc_final: 0.7418 (mmm-85) REVERT: O 169 GLU cc_start: 0.7173 (pm20) cc_final: 0.6861 (pm20) REVERT: O 170 LYS cc_start: 0.8037 (ptpt) cc_final: 0.7191 (tppt) REVERT: O 175 ARG cc_start: 0.7287 (mtt-85) cc_final: 0.6895 (mtt180) outliers start: 21 outliers final: 15 residues processed: 99 average time/residue: 0.1428 time to fit residues: 20.6685 Evaluate side-chains 100 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain O residue 174 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 118 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 95 optimal weight: 50.0000 chunk 38 optimal weight: 0.9990 chunk 140 optimal weight: 0.0060 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 ASN L 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.145595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.097510 restraints weight = 37308.956| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.38 r_work: 0.3332 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16441 Z= 0.118 Angle : 0.517 10.159 23529 Z= 0.290 Chirality : 0.036 0.266 2870 Planarity : 0.005 0.068 2018 Dihedral : 23.493 170.172 5573 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.34 % Favored : 96.50 % Rotamer: Outliers : 2.23 % Allowed : 10.34 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.05 (0.24), residues: 1227 helix: 1.09 (0.22), residues: 591 sheet: -0.66 (0.45), residues: 129 loop : -1.01 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 377 TYR 0.011 0.001 TYR A 894 PHE 0.020 0.001 PHE A 883 TRP 0.012 0.001 TRP A 547 HIS 0.005 0.001 HIS A1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (16441) covalent geometry : angle 0.51717 / 0.29 (23529) hydrogen bonds : bond 0.04795 / 3.26 ( 575) hydrogen bonds : angle 3.92047 / 2.84 ( 1569) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8254 (mm-30) REVERT: A 95 ASN cc_start: 0.8158 (t0) cc_final: 0.7656 (t0) REVERT: A 139 LEU cc_start: 0.5926 (tp) cc_final: 0.5557 (mp) REVERT: A 159 PHE cc_start: 0.7109 (m-80) cc_final: 0.6755 (m-10) REVERT: A 1017 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8643 (mp) REVERT: L 32 ARG cc_start: 0.6150 (mtp180) cc_final: 0.5531 (ttt-90) REVERT: L 64 LEU cc_start: 0.5280 (tp) cc_final: 0.4975 (mt) REVERT: L 86 LEU cc_start: 0.7079 (mt) cc_final: 0.6793 (tp) REVERT: M 117 LYS cc_start: 0.6738 (mttt) cc_final: 0.6465 (mtpt) REVERT: O 168 GLU cc_start: 0.6751 (pt0) cc_final: 0.6443 (pt0) REVERT: O 169 GLU cc_start: 0.7174 (pm20) cc_final: 0.6784 (pm20) REVERT: O 170 LYS cc_start: 0.7949 (ptpt) cc_final: 0.7137 (tppt) REVERT: O 175 ARG cc_start: 0.7276 (mtt-85) cc_final: 0.6892 (mtt180) outliers start: 24 outliers final: 15 residues processed: 104 average time/residue: 0.1452 time to fit residues: 21.9181 Evaluate side-chains 99 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain O residue 150 THR Chi-restraints excluded: chain O residue 174 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 11 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 95 optimal weight: 50.0000 chunk 9 optimal weight: 0.8980 chunk 113 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.144634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.094031 restraints weight = 37061.267| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.22 r_work: 0.3329 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16441 Z= 0.134 Angle : 0.533 11.043 23529 Z= 0.296 Chirality : 0.036 0.262 2870 Planarity : 0.005 0.067 2018 Dihedral : 23.479 168.755 5573 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.67 % Favored : 96.17 % Rotamer: Outliers : 2.05 % Allowed : 10.52 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.07 (0.24), residues: 1227 helix: 1.09 (0.21), residues: 591 sheet: -0.62 (0.45), residues: 129 loop : -0.98 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 82 TYR 0.018 0.001 TYR A 894 PHE 0.016 0.002 PHE A 331 TRP 0.011 0.001 TRP A 547 HIS 0.005 0.001 HIS A1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (16441) covalent geometry : angle 0.53272 / 0.30 (23529) hydrogen bonds : bond 0.05127 / 3.48 ( 575) hydrogen bonds : angle 3.99930 / 2.90 ( 1569) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8223 (mm-30) REVERT: A 95 ASN cc_start: 0.8162 (t0) cc_final: 0.7656 (t0) REVERT: A 139 LEU cc_start: 0.5945 (tp) cc_final: 0.5695 (mp) REVERT: A 159 PHE cc_start: 0.7096 (m-80) cc_final: 0.6826 (m-80) REVERT: A 372 MET cc_start: 0.1791 (tpt) cc_final: 0.1470 (tpp) REVERT: A 1017 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8867 (mp) REVERT: L 32 ARG cc_start: 0.6047 (mtp180) cc_final: 0.5449 (ttt-90) REVERT: L 64 LEU cc_start: 0.5311 (tp) cc_final: 0.5015 (mt) REVERT: L 86 LEU cc_start: 0.7059 (mt) cc_final: 0.6766 (tp) REVERT: M 117 LYS cc_start: 0.6691 (mttt) cc_final: 0.6365 (mtpt) REVERT: O 168 GLU cc_start: 0.6762 (pt0) cc_final: 0.6454 (pt0) REVERT: O 169 GLU cc_start: 0.7200 (pm20) cc_final: 0.6799 (pm20) REVERT: O 170 LYS cc_start: 0.7977 (ptpt) cc_final: 0.7151 (tppt) REVERT: O 175 ARG cc_start: 0.7229 (mtt-85) cc_final: 0.6990 (mtt180) outliers start: 22 outliers final: 15 residues processed: 92 average time/residue: 0.1511 time to fit residues: 19.9023 Evaluate side-chains 98 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain O residue 174 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 119 optimal weight: 50.0000 chunk 73 optimal weight: 0.0060 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 96 optimal weight: 40.0000 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 113 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.145609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.095354 restraints weight = 37532.432| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.25 r_work: 0.3345 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16441 Z= 0.114 Angle : 0.511 11.117 23529 Z= 0.284 Chirality : 0.035 0.253 2870 Planarity : 0.004 0.066 2018 Dihedral : 23.450 169.658 5573 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.67 % Favored : 96.17 % Rotamer: Outliers : 1.49 % Allowed : 11.17 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.20 (0.24), residues: 1227 helix: 1.18 (0.22), residues: 594 sheet: -0.50 (0.45), residues: 129 loop : -0.92 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 72 TYR 0.024 0.001 TYR A 894 PHE 0.013 0.001 PHE A 331 TRP 0.011 0.001 TRP A 547 HIS 0.004 0.001 HIS A1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (16441) covalent geometry : angle 0.51100 / 0.28 (23529) hydrogen bonds : bond 0.04645 / 3.14 ( 575) hydrogen bonds : angle 3.84765 / 2.78 ( 1569) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8211 (mm-30) REVERT: A 95 ASN cc_start: 0.8107 (t0) cc_final: 0.7613 (t0) REVERT: A 139 LEU cc_start: 0.5966 (tp) cc_final: 0.5708 (mp) REVERT: A 159 PHE cc_start: 0.6984 (m-80) cc_final: 0.6723 (m-10) REVERT: A 970 MET cc_start: 0.8367 (ttm) cc_final: 0.7959 (ttt) REVERT: A 1017 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8828 (mp) REVERT: L 26 PHE cc_start: 0.6120 (m-80) cc_final: 0.5863 (m-80) REVERT: L 32 ARG cc_start: 0.5918 (mtp180) cc_final: 0.5340 (ttt-90) REVERT: L 86 LEU cc_start: 0.7030 (mt) cc_final: 0.6745 (tp) REVERT: M 52 ASP cc_start: 0.7830 (p0) cc_final: 0.7590 (p0) REVERT: M 117 LYS cc_start: 0.6539 (mttt) cc_final: 0.6274 (mtpt) REVERT: O 154 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6634 (ptt90) REVERT: O 169 GLU cc_start: 0.7216 (pm20) cc_final: 0.6824 (pm20) REVERT: O 170 LYS cc_start: 0.8015 (ptpt) cc_final: 0.7186 (tppt) outliers start: 16 outliers final: 13 residues processed: 91 average time/residue: 0.1550 time to fit residues: 20.1531 Evaluate side-chains 94 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 74 ASN Chi-restraints excluded: chain O residue 154 ARG Chi-restraints excluded: chain O residue 174 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.146028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.096051 restraints weight = 37420.489| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.22 r_work: 0.3359 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16441 Z= 0.105 Angle : 0.502 11.051 23529 Z= 0.280 Chirality : 0.035 0.245 2870 Planarity : 0.004 0.065 2018 Dihedral : 23.418 170.063 5573 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.83 % Favored : 96.01 % Rotamer: Outliers : 1.77 % Allowed : 11.17 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.24), residues: 1227 helix: 1.28 (0.22), residues: 594 sheet: -0.39 (0.46), residues: 129 loop : -0.85 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 82 TYR 0.033 0.001 TYR A 894 PHE 0.013 0.001 PHE A 331 TRP 0.012 0.001 TRP A 547 HIS 0.004 0.001 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (16441) covalent geometry : angle 0.50247 / 0.28 (23529) hydrogen bonds : bond 0.04432 / 3.00 ( 575) hydrogen bonds : angle 3.77951 / 2.73 ( 1569) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8223 (mm-30) REVERT: A 95 ASN cc_start: 0.8113 (t0) cc_final: 0.7622 (t0) REVERT: A 159 PHE cc_start: 0.6956 (m-80) cc_final: 0.6734 (m-80) REVERT: A 1017 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8754 (mp) REVERT: L 32 ARG cc_start: 0.5893 (mtp180) cc_final: 0.5330 (ttt-90) REVERT: L 64 LEU cc_start: 0.5325 (tp) cc_final: 0.5033 (mt) REVERT: L 86 LEU cc_start: 0.7031 (mt) cc_final: 0.6745 (tp) REVERT: M 117 LYS cc_start: 0.6503 (mttt) cc_final: 0.6264 (mtpt) REVERT: O 169 GLU cc_start: 0.7241 (pm20) cc_final: 0.6735 (pm20) REVERT: O 170 LYS cc_start: 0.7924 (ptpt) cc_final: 0.7152 (tppt) outliers start: 19 outliers final: 17 residues processed: 95 average time/residue: 0.1497 time to fit residues: 20.4660 Evaluate side-chains 100 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain O residue 154 ARG Chi-restraints excluded: chain O residue 174 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 71 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 42 optimal weight: 0.4980 chunk 114 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 106 optimal weight: 30.0000 chunk 73 optimal weight: 0.0000 chunk 11 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.144160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.093479 restraints weight = 37264.826| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.22 r_work: 0.3319 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16441 Z= 0.152 Angle : 0.554 11.550 23529 Z= 0.303 Chirality : 0.036 0.243 2870 Planarity : 0.005 0.065 2018 Dihedral : 23.424 167.823 5573 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.99 % Favored : 95.84 % Rotamer: Outliers : 2.05 % Allowed : 11.27 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.13 (0.24), residues: 1227 helix: 1.07 (0.21), residues: 600 sheet: -0.38 (0.46), residues: 127 loop : -0.95 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 82 TYR 0.010 0.001 TYR A 638 PHE 0.017 0.002 PHE A 331 TRP 0.010 0.001 TRP A 547 HIS 0.005 0.001 HIS A1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (16441) covalent geometry : angle 0.55407 / 0.30 (23529) hydrogen bonds : bond 0.05400 / 3.66 ( 575) hydrogen bonds : angle 3.99707 / 2.89 ( 1569) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8213 (mm-30) REVERT: A 95 ASN cc_start: 0.8154 (t0) cc_final: 0.7663 (t0) REVERT: A 159 PHE cc_start: 0.7137 (m-80) cc_final: 0.6907 (m-80) REVERT: A 866 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8283 (tp) REVERT: A 970 MET cc_start: 0.8421 (ttm) cc_final: 0.7933 (ttt) REVERT: A 1017 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8937 (mp) REVERT: L 32 ARG cc_start: 0.5901 (mtp180) cc_final: 0.5281 (ttt-90) REVERT: L 64 LEU cc_start: 0.5348 (tp) cc_final: 0.5073 (mt) REVERT: L 86 LEU cc_start: 0.6984 (mt) cc_final: 0.6683 (tp) REVERT: M 117 LYS cc_start: 0.6506 (mttt) cc_final: 0.6238 (mtpt) REVERT: O 170 LYS cc_start: 0.7951 (ptpt) cc_final: 0.7119 (tppt) outliers start: 22 outliers final: 18 residues processed: 94 average time/residue: 0.1496 time to fit residues: 20.0459 Evaluate side-chains 97 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain O residue 154 ARG Chi-restraints excluded: chain O residue 174 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 81 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 0.0570 chunk 86 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 87 optimal weight: 0.0670 chunk 68 optimal weight: 4.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.145579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.095322 restraints weight = 37190.921| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.22 r_work: 0.3356 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 16441 Z= 0.106 Angle : 0.510 11.138 23529 Z= 0.281 Chirality : 0.035 0.307 2870 Planarity : 0.004 0.065 2018 Dihedral : 23.403 169.715 5573 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.42 % Favored : 96.41 % Rotamer: Outliers : 1.58 % Allowed : 11.82 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.24), residues: 1227 helix: 1.19 (0.22), residues: 601 sheet: -0.34 (0.45), residues: 129 loop : -0.79 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 82 TYR 0.019 0.001 TYR A 894 PHE 0.012 0.001 PHE A 331 TRP 0.011 0.001 TRP A 547 HIS 0.003 0.001 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (16441) covalent geometry : angle 0.51030 / 0.28 (23529) hydrogen bonds : bond 0.04418 / 2.95 ( 575) hydrogen bonds : angle 3.80462 / 2.74 ( 1569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4592.36 seconds wall clock time: 79 minutes 9.56 seconds (4749.56 seconds total)