Starting phenix.real_space_refine on Thu Aug 6 14:59:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qaz_52980/08_2026/9qaz_52980.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qaz_52980/08_2026/9qaz_52980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qaz_52980/08_2026/9qaz_52980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qaz_52980/08_2026/9qaz_52980.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qaz_52980/08_2026/9qaz_52980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qaz_52980/08_2026/9qaz_52980.map" } resolution = 3.6 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: 5 Type Number sf(0) Gaussians P 260 5.49 5 S 42 5.16 5 C 8819 2.51 5 N 2812 2.21 5 O 3538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15471 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': 18, 'rna3p_pur': 99, 'rna3p_pyr': 119} Link IDs: {'rna2p': 35, 'rna3p': 217} 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: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} 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: 2.79, per 1000 atoms: 0.18 Number of scatterers: 15471 At special positions: 0 Unit cell: (167.322, 123.903, 145.083, 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 260 15.00 O 3538 8.00 N 2812 7.00 C 8819 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: 1.11 Conformation dependent library (CDL) restraints added in 462.3 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 54.1% alpha, 12.7% beta 71 base pairs and 125 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 removed outlier: 3.898A 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: 3.587A pdb=" N VAL A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 92 removed outlier: 3.580A pdb=" N VAL A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 removed outlier: 3.847A pdb=" N GLY A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.797A pdb=" N ARG A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.737A 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: 3.648A pdb=" N PHE A 393 " --> pdb=" O MET A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.504A pdb=" N LEU A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 454 removed outlier: 3.507A pdb=" N ARG A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 473 removed outlier: 3.910A pdb=" N ARG A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.707A pdb=" N TRP A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 497 removed outlier: 3.504A pdb=" N GLU A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.684A pdb=" N LEU A 520 " --> pdb=" O CYS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 551 removed outlier: 3.525A pdb=" N LYS A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 removed outlier: 3.627A pdb=" N PHE A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 597 removed outlier: 3.713A pdb=" N LYS A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 596 " --> pdb=" O HIS A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.664A pdb=" N GLU A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 672 removed outlier: 4.081A 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: 3.832A pdb=" N THR A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 734 removed outlier: 3.653A pdb=" N GLU A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 733 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 769 removed outlier: 3.575A 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: 3.661A pdb=" N CYS A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 843 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 3.611A 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: 3.680A pdb=" N ALA A 880 " --> pdb=" O HIS A 876 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 890 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 950 removed outlier: 3.602A pdb=" N TYR A 949 " --> pdb=" O TYR A 946 " (cutoff:3.500A) removed outlier: 3.502A 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: 3.547A 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: 3.546A pdb=" N LEU A1007 " --> pdb=" O LYS A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1028 removed outlier: 3.541A pdb=" N LYS A1027 " --> pdb=" O GLN A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1051 removed outlier: 3.552A pdb=" N ASP A1038 " --> pdb=" O ARG A1034 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS A1043 " --> pdb=" O THR A1039 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A1051 " --> pdb=" O LEU A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1085 removed outlier: 3.898A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS A1075 " --> pdb=" O GLN A1071 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR A1083 " --> pdb=" O LEU A1079 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.606A pdb=" N TYR A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) Proline residue: A1091 - end of helix removed outlier: 4.091A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN A1102 " --> pdb=" O THR A1098 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A1106 " --> pdb=" O GLN A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1119 removed outlier: 3.875A pdb=" N THR A1113 " --> pdb=" O GLY A1109 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 38 removed outlier: 4.400A pdb=" N LEU L 34 " --> pdb=" O ARG L 30 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU L 35 " --> pdb=" O VAL L 31 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY L 38 " --> pdb=" O LEU L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 73 removed outlier: 3.600A pdb=" N GLU L 57 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU L 66 " --> pdb=" O GLU L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 91 removed outlier: 3.961A pdb=" N LEU L 84 " --> pdb=" O ILE L 80 " (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: 3.635A pdb=" N ASN L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS L 96 " --> pdb=" O GLU L 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 50 removed outlier: 3.627A pdb=" N VAL M 45 " --> pdb=" O TYR M 41 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS M 47 " --> pdb=" O TYR M 43 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN M 48 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 3.639A 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: 3.621A pdb=" N PHE M 66 " --> pdb=" O ILE M 62 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE M 70 " --> pdb=" O PHE M 66 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS M 83 " --> pdb=" O SER M 79 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR M 84 " --> pdb=" O ARG M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 103 removed outlier: 3.782A pdb=" N ILE M 95 " --> pdb=" O THR M 91 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN M 96 " --> pdb=" O SER M 92 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N THR M 97 " --> pdb=" O ARG M 93 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG M 100 " --> pdb=" O GLN M 96 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU M 103 " --> pdb=" O VAL M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 125 removed outlier: 3.757A pdb=" N SER M 113 " --> pdb=" O LYS M 109 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU M 114 " --> pdb=" O HIS M 110 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY M 115 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR M 120 " --> pdb=" O THR M 116 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER M 125 " --> pdb=" O LYS M 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 104 removed outlier: 3.843A pdb=" N ILE O 103 " --> pdb=" O ILE O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 164 removed outlier: 3.622A pdb=" N LEU O 162 " --> pdb=" O THR O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 238 removed outlier: 3.504A pdb=" N LYS O 232 " --> pdb=" O LEU O 228 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS O 233 " --> pdb=" O ASP O 229 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR O 235 " --> pdb=" O GLN O 231 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP O 236 " --> pdb=" O LYS O 232 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS O 237 " --> pdb=" O LYS O 233 " (cutoff:3.500A) removed outlier: 4.439A 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: 3.772A pdb=" N ALA A 157 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 11.340A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER A 796 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.701A 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: 3.772A pdb=" N ALA A 157 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 11.340A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER A 796 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A 741 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 3.518A 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: 7.308A pdb=" N LEU A 617 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ARG A 819 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.337A 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: 3.718A pdb=" N LEU A 866 " --> pdb=" O ASP A 869 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP A 869 " --> pdb=" O LEU A 866 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 711 " --> pdb=" O PHE A 870 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 709 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 3.559A 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: 7.216A pdb=" N LEU O 145 " --> pdb=" O LEU O 118 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL O 120 " --> pdb=" O THR O 143 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N THR O 143 " --> pdb=" O VAL O 120 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N LEU O 204 " --> pdb=" O SER O 152 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ARG O 154 " --> pdb=" O LEU O 204 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL O 206 " --> pdb=" O ARG O 154 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU O 156 " --> pdb=" O VAL O 206 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 187 hydrogen bonds 346 hydrogen bond angles 0 basepair planarities 71 basepair parallelities 125 stacking parallelities Total time for adding SS restraints: 4.23 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1941 1.31 - 1.44: 5740 1.44 - 1.57: 8071 1.57 - 1.70: 516 1.70 - 1.83: 55 Bond restraints: 16323 Sorted by residual: bond pdb=" C GLN A 454 " pdb=" O GLN A 454 " ideal model delta sigma weight residual 1.233 1.185 0.049 1.06e-02 8.90e+03 2.11e+01 bond pdb=" C4' U B 307 " pdb=" O4' U B 307 " ideal model delta sigma weight residual 1.454 1.423 0.031 1.00e-02 1.00e+04 9.74e+00 bond pdb=" CG ARG A 378 " pdb=" CD ARG A 378 " ideal model delta sigma weight residual 1.520 1.428 0.092 3.00e-02 1.11e+03 9.31e+00 bond pdb=" CA PRO A1020 " pdb=" CB PRO A1020 " ideal model delta sigma weight residual 1.533 1.490 0.043 1.42e-02 4.96e+03 9.20e+00 bond pdb=" CZ ARG L 33 " pdb=" NH2 ARG L 33 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 8.98e+00 ... (remaining 16318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 22172 2.55 - 5.10: 1124 5.10 - 7.64: 43 7.64 - 10.19: 4 10.19 - 12.74: 3 Bond angle restraints: 23346 Sorted by residual: angle pdb=" O3' C B 119 " pdb=" P G B 120 " pdb=" O5' G B 120 " ideal model delta sigma weight residual 104.00 91.26 12.74 1.90e+00 2.77e-01 4.50e+01 angle pdb=" O6 G B 58 " pdb=" C6 G B 58 " pdb=" N1 G B 58 " ideal model delta sigma weight residual 119.90 116.10 3.80 6.00e-01 2.78e+00 4.01e+01 angle pdb=" C LYS A 338 " pdb=" CA LYS A 338 " pdb=" CB LYS A 338 " ideal model delta sigma weight residual 109.84 101.84 8.00 1.50e+00 4.44e-01 2.84e+01 angle pdb=" CA LYS A 338 " pdb=" C LYS A 338 " pdb=" O LYS A 338 " ideal model delta sigma weight residual 120.96 116.03 4.93 1.09e+00 8.42e-01 2.05e+01 angle pdb=" O4' A B 176 " pdb=" C4' A B 176 " pdb=" C3' A B 176 " ideal model delta sigma weight residual 106.10 102.51 3.59 8.00e-01 1.56e+00 2.01e+01 ... (remaining 23341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 9451 35.74 - 71.49: 702 71.49 - 107.23: 112 107.23 - 142.98: 8 142.98 - 178.72: 11 Dihedral angle restraints: 10284 sinusoidal: 6663 harmonic: 3621 Sorted by residual: 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 74.89 72.11 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" C4' G B 300 " pdb=" C3' G B 300 " pdb=" C2' G B 300 " pdb=" C1' G B 300 " ideal model delta sinusoidal sigma weight residual -35.00 35.26 -70.26 1 8.00e+00 1.56e-02 9.93e+01 dihedral pdb=" C4' U B 307 " pdb=" C3' U B 307 " pdb=" C2' U B 307 " pdb=" C1' U B 307 " ideal model delta sinusoidal sigma weight residual -35.00 34.78 -69.78 1 8.00e+00 1.56e-02 9.82e+01 ... (remaining 10281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2498 0.119 - 0.237: 335 0.237 - 0.356: 12 0.356 - 0.475: 2 0.475 - 0.593: 3 Chirality restraints: 2850 Sorted by residual: chirality pdb=" P DG N 24 " pdb=" OP1 DG N 24 " pdb=" OP2 DG N 24 " pdb=" O5' DG N 24 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.59 2.00e-01 2.50e+01 8.80e+00 chirality pdb=" P G B 163 " pdb=" OP1 G B 163 " pdb=" OP2 G B 163 " pdb=" O5' G B 163 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 6.95e+00 chirality pdb=" P C B 238 " pdb=" OP1 C B 238 " pdb=" OP2 C B 238 " pdb=" O5' C B 238 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.87e+00 ... (remaining 2847 not shown) Planarity restraints: 2013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 142 " -0.206 2.00e-02 2.50e+03 1.06e-01 2.52e+02 pdb=" N1 C B 142 " 0.050 2.00e-02 2.50e+03 pdb=" C2 C B 142 " 0.056 2.00e-02 2.50e+03 pdb=" O2 C B 142 " 0.053 2.00e-02 2.50e+03 pdb=" N3 C B 142 " 0.006 2.00e-02 2.50e+03 pdb=" C4 C B 142 " 0.057 2.00e-02 2.50e+03 pdb=" N4 C B 142 " -0.180 2.00e-02 2.50e+03 pdb=" C5 C B 142 " 0.070 2.00e-02 2.50e+03 pdb=" C6 C B 142 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 307 " -0.089 2.00e-02 2.50e+03 5.23e-02 6.15e+01 pdb=" N1 U B 307 " 0.086 2.00e-02 2.50e+03 pdb=" C2 U B 307 " 0.006 2.00e-02 2.50e+03 pdb=" O2 U B 307 " 0.050 2.00e-02 2.50e+03 pdb=" N3 U B 307 " -0.061 2.00e-02 2.50e+03 pdb=" C4 U B 307 " -0.015 2.00e-02 2.50e+03 pdb=" O4 U B 307 " -0.016 2.00e-02 2.50e+03 pdb=" C5 U B 307 " 0.049 2.00e-02 2.50e+03 pdb=" C6 U B 307 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 291 " -0.035 2.00e-02 2.50e+03 3.65e-02 3.00e+01 pdb=" N1 U B 291 " 0.019 2.00e-02 2.50e+03 pdb=" C2 U B 291 " -0.036 2.00e-02 2.50e+03 pdb=" O2 U B 291 " 0.066 2.00e-02 2.50e+03 pdb=" N3 U B 291 " -0.051 2.00e-02 2.50e+03 pdb=" C4 U B 291 " 0.010 2.00e-02 2.50e+03 pdb=" O4 U B 291 " -0.010 2.00e-02 2.50e+03 pdb=" C5 U B 291 " 0.043 2.00e-02 2.50e+03 pdb=" C6 U B 291 " -0.005 2.00e-02 2.50e+03 ... (remaining 2010 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 4 2.03 - 2.75: 1149 2.75 - 3.47: 20457 3.47 - 4.18: 39942 4.18 - 4.90: 60697 Nonbonded interactions: 122249 Sorted by model distance: nonbonded pdb=" O TRP A 510 " pdb=" O2' C B 313 " model vdw 1.313 3.040 nonbonded pdb=" OG SER A 12 " pdb=" O2' A B 61 " model vdw 1.827 3.040 nonbonded pdb=" CA HIS A 752 " pdb=" O6 G B 58 " model vdw 1.869 3.470 nonbonded pdb=" C HIS A 752 " pdb=" O6 G B 58 " model vdw 2.026 3.270 nonbonded pdb=" O PHE A1021 " pdb=" O2' U B 312 " model vdw 2.051 3.040 ... (remaining 122244 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 group one per residue 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: 1.830 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.790 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 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 : 0.009 0.092 16323 Z= 0.617 Angle : 1.210 12.740 23346 Z= 0.839 Chirality : 0.080 0.593 2850 Planarity : 0.012 0.149 2013 Dihedral : 22.034 178.722 7938 Min Nonbonded Distance : 1.313 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.28 % Favored : 93.32 % Rotamer: Outliers : 0.09 % Allowed : 1.96 % Favored : 97.95 % Cbeta Deviations : 0.09 % 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: -3.06 (0.19), residues: 1227 helix: -1.82 (0.17), residues: 545 sheet: -1.95 (0.43), residues: 106 loop : -2.19 (0.22), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.003 ARG A 470 TYR 0.057 0.007 TYR A 576 PHE 0.056 0.008 PHE A 708 TRP 0.052 0.010 TRP A 547 HIS 0.020 0.004 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00883 / 0.62 (16323) covalent geometry : angle 1.21013 / 0.84 (23346) hydrogen bonds : bond 0.27646 / 18.92 ( 630) hydrogen bonds : angle 8.37545 / 5.91 ( 1666) *********************** 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 190 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7969 (tp30) REVERT: A 384 GLN cc_start: 0.7157 (tt0) cc_final: 0.6572 (pm20) REVERT: A 395 GLU cc_start: 0.9577 (tt0) cc_final: 0.9359 (tm-30) REVERT: A 399 ASN cc_start: 0.8169 (m-40) cc_final: 0.7852 (m110) REVERT: A 489 ARG cc_start: 0.9055 (ttm-80) cc_final: 0.8818 (mmp80) REVERT: A 555 GLU cc_start: 0.8815 (tp30) cc_final: 0.8341 (tp30) REVERT: A 580 VAL cc_start: 0.7367 (p) cc_final: 0.6942 (m) REVERT: A 775 GLN cc_start: 0.8457 (mt0) cc_final: 0.8218 (mp10) REVERT: A 900 LEU cc_start: 0.8477 (mp) cc_final: 0.8031 (tt) REVERT: L 63 ILE cc_start: 0.6042 (tt) cc_final: 0.5610 (pt) REVERT: L 75 LYS cc_start: 0.6533 (tptt) cc_final: 0.6277 (ttpp) REVERT: M 50 HIS cc_start: 0.5946 (m-70) cc_final: 0.5599 (m170) REVERT: M 63 MET cc_start: 0.8680 (mtt) cc_final: 0.7844 (tpt) REVERT: M 66 PHE cc_start: 0.8166 (m-80) cc_final: 0.7607 (m-80) REVERT: O 98 TRP cc_start: 0.7390 (p-90) cc_final: 0.6866 (p-90) REVERT: O 154 ARG cc_start: 0.5176 (ttp80) cc_final: 0.4966 (tmt-80) REVERT: O 159 ARG cc_start: 0.8252 (ttt180) cc_final: 0.7942 (mmm160) REVERT: O 169 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7147 (mp0) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.1424 time to fit residues: 36.6701 Evaluate side-chains 96 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 50.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.0570 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.0470 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 GLN A 460 GLN A 879 HIS ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN L 74 ASN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 116 GLN ** O 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.116240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.097539 restraints weight = 78857.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.097785 restraints weight = 59174.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.097823 restraints weight = 40715.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.098107 restraints weight = 39660.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.098168 restraints weight = 34352.321| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 16323 Z= 0.172 Angle : 0.699 10.595 23346 Z= 0.382 Chirality : 0.044 0.562 2850 Planarity : 0.006 0.089 2013 Dihedral : 23.955 174.762 5519 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.58 % Rotamer: Outliers : 1.21 % Allowed : 6.42 % Favored : 92.36 % 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: -1.35 (0.21), residues: 1227 helix: 0.05 (0.20), residues: 575 sheet: -1.81 (0.41), residues: 128 loop : -1.67 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 885 TYR 0.018 0.002 TYR A 739 PHE 0.017 0.003 PHE A 544 TRP 0.031 0.003 TRP O 167 HIS 0.008 0.002 HIS O 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (16323) covalent geometry : angle 0.69943 / 0.38 (23346) hydrogen bonds : bond 0.07432 / 5.25 ( 630) hydrogen bonds : angle 4.92188 / 3.55 ( 1666) *********************** 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 126 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 75 LYS cc_start: 0.6632 (tptt) cc_final: 0.6420 (ttpp) outliers start: 13 outliers final: 8 residues processed: 123 average time/residue: 0.1192 time to fit residues: 21.2782 Evaluate side-chains 81 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain M residue 96 GLN Chi-restraints excluded: chain O residue 150 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 141 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 135 optimal weight: 30.0000 chunk 60 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN A1013 HIS A1023 GLN ** A1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.108713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.087339 restraints weight = 76036.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.087180 restraints weight = 57322.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.087535 restraints weight = 42099.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.087515 restraints weight = 36851.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.087633 restraints weight = 36529.348| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 16323 Z= 0.286 Angle : 0.878 11.319 23346 Z= 0.458 Chirality : 0.052 0.567 2850 Planarity : 0.008 0.084 2013 Dihedral : 23.919 176.754 5519 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.32 % Favored : 95.44 % Rotamer: Outliers : 2.79 % Allowed : 9.40 % Favored : 87.80 % 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: -1.40 (0.22), residues: 1227 helix: -0.34 (0.20), residues: 570 sheet: -1.01 (0.46), residues: 117 loop : -1.48 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG O 96 TYR 0.023 0.003 TYR A 576 PHE 0.039 0.004 PHE A 708 TRP 0.049 0.004 TRP O 167 HIS 0.016 0.003 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.29 (16323) covalent geometry : angle 0.87821 / 0.46 (23346) hydrogen bonds : bond 0.08567 / 6.50 ( 630) hydrogen bonds : angle 5.09939 / 3.69 ( 1666) *********************** 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 104 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 MET cc_start: 0.1027 (mpp) cc_final: 0.0730 (mpp) REVERT: A 395 GLU cc_start: 0.5891 (tm-30) cc_final: 0.5680 (tp30) REVERT: A 399 ASN cc_start: 0.5257 (m-40) cc_final: 0.4852 (m-40) REVERT: L 75 LYS cc_start: 0.6602 (tptt) cc_final: 0.6390 (ttpp) outliers start: 30 outliers final: 24 residues processed: 104 average time/residue: 0.1160 time to fit residues: 17.7528 Evaluate side-chains 86 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 96 GLN Chi-restraints excluded: chain O residue 150 THR Chi-restraints excluded: chain O residue 167 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 115 optimal weight: 40.0000 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 140 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 50.0000 chunk 90 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 GLN ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 HIS A 983 HIS ** M 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.110540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.089424 restraints weight = 75790.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.089011 restraints weight = 50498.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.089452 restraints weight = 41089.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.089265 restraints weight = 35057.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.089428 restraints weight = 34174.696| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16323 Z= 0.129 Angle : 0.597 9.699 23346 Z= 0.323 Chirality : 0.039 0.343 2850 Planarity : 0.005 0.064 2013 Dihedral : 23.827 175.511 5519 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.18 % Favored : 96.66 % Rotamer: Outliers : 2.42 % Allowed : 10.52 % 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: -0.61 (0.23), residues: 1227 helix: 0.47 (0.21), residues: 567 sheet: -0.74 (0.46), residues: 119 loop : -1.23 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 73 TYR 0.018 0.001 TYR A 739 PHE 0.014 0.002 PHE O 172 TRP 0.037 0.002 TRP O 167 HIS 0.006 0.001 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (16323) covalent geometry : angle 0.59745 / 0.32 (23346) hydrogen bonds : bond 0.05680 / 4.10 ( 630) hydrogen bonds : angle 4.35259 / 3.10 ( 1666) *********************** 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 89 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 75 LYS cc_start: 0.6630 (tptt) cc_final: 0.6356 (ttpp) outliers start: 26 outliers final: 17 residues processed: 85 average time/residue: 0.1257 time to fit residues: 15.3148 Evaluate side-chains 74 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 72 ARG Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 96 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 105 optimal weight: 30.0000 chunk 18 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 47 optimal weight: 0.6980 chunk 134 optimal weight: 0.0870 chunk 79 optimal weight: 0.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 85 ASN ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.110731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.089980 restraints weight = 75894.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.089729 restraints weight = 57000.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.090220 restraints weight = 42170.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.090051 restraints weight = 36674.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.090223 restraints weight = 37232.209| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16323 Z= 0.119 Angle : 0.557 9.695 23346 Z= 0.301 Chirality : 0.038 0.341 2850 Planarity : 0.004 0.059 2013 Dihedral : 23.724 179.384 5519 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.50 % Favored : 96.25 % Rotamer: Outliers : 2.33 % Allowed : 11.55 % Favored : 86.13 % 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: -0.22 (0.23), residues: 1227 helix: 0.78 (0.21), residues: 583 sheet: -0.50 (0.47), residues: 119 loop : -1.06 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 73 TYR 0.018 0.001 TYR A 772 PHE 0.028 0.001 PHE M 66 TRP 0.036 0.002 TRP O 167 HIS 0.011 0.001 HIS O 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (16323) covalent geometry : angle 0.55689 / 0.30 (23346) hydrogen bonds : bond 0.05142 / 3.82 ( 630) hydrogen bonds : angle 4.07926 / 2.88 ( 1666) *********************** 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 90 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 64 ASN cc_start: 0.8391 (m110) cc_final: 0.7782 (m110) outliers start: 25 outliers final: 16 residues processed: 86 average time/residue: 0.1296 time to fit residues: 16.0925 Evaluate side-chains 74 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 96 GLN Chi-restraints excluded: chain O residue 167 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 108 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 137 optimal weight: 0.0010 chunk 75 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 ASN M 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.110989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.090628 restraints weight = 75450.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.090127 restraints weight = 54456.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.090080 restraints weight = 44679.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.090233 restraints weight = 44602.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.090324 restraints weight = 38144.037| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16323 Z= 0.112 Angle : 0.539 11.926 23346 Z= 0.291 Chirality : 0.037 0.339 2850 Planarity : 0.004 0.057 2013 Dihedral : 23.692 175.283 5519 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.50 % Favored : 96.25 % Rotamer: Outliers : 1.77 % Allowed : 11.73 % Favored : 86.50 % 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: 0.91 (0.21), residues: 581 sheet: -0.28 (0.48), residues: 119 loop : -1.00 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 859 TYR 0.010 0.001 TYR A 739 PHE 0.017 0.001 PHE M 71 TRP 0.030 0.002 TRP O 167 HIS 0.006 0.001 HIS O 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (16323) covalent geometry : angle 0.53929 / 0.29 (23346) hydrogen bonds : bond 0.04911 / 3.64 ( 630) hydrogen bonds : angle 3.99756 / 2.80 ( 1666) *********************** 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 81 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 64 ASN cc_start: 0.8416 (m110) cc_final: 0.7723 (m110) outliers start: 19 outliers final: 16 residues processed: 76 average time/residue: 0.1352 time to fit residues: 14.9110 Evaluate side-chains 75 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 72 ARG Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 60 MET Chi-restraints excluded: chain M residue 96 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 12 optimal weight: 4.9990 chunk 105 optimal weight: 30.0000 chunk 59 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 143 optimal weight: 30.0000 chunk 30 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.109160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.088299 restraints weight = 74904.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.088572 restraints weight = 57118.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.088816 restraints weight = 40350.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.088784 restraints weight = 35398.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.088860 restraints weight = 34466.825| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 16323 Z= 0.161 Angle : 0.592 9.876 23346 Z= 0.316 Chirality : 0.039 0.334 2850 Planarity : 0.005 0.070 2013 Dihedral : 23.732 169.507 5519 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.32 % Favored : 95.35 % Rotamer: Outliers : 1.86 % Allowed : 12.76 % Favored : 85.38 % 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: -0.15 (0.23), residues: 1227 helix: 0.82 (0.21), residues: 580 sheet: -0.00 (0.52), residues: 109 loop : -1.11 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 938 TYR 0.013 0.001 TYR A 739 PHE 0.016 0.002 PHE O 172 TRP 0.027 0.002 TRP O 167 HIS 0.007 0.002 HIS A 925 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (16323) covalent geometry : angle 0.59189 / 0.32 (23346) hydrogen bonds : bond 0.05309 / 3.95 ( 630) hydrogen bonds : angle 4.14379 / 2.92 ( 1666) *********************** 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 81 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 64 ASN cc_start: 0.8159 (m110) cc_final: 0.7540 (m110) outliers start: 20 outliers final: 18 residues processed: 76 average time/residue: 0.1305 time to fit residues: 14.3251 Evaluate side-chains 73 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 72 ARG Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain O residue 167 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 121 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 105 optimal weight: 30.0000 chunk 106 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 546 HIS M 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.108879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.087827 restraints weight = 74980.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.088416 restraints weight = 54746.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.088675 restraints weight = 38384.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.088376 restraints weight = 32640.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.088457 restraints weight = 34636.929| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16323 Z= 0.142 Angle : 0.571 13.789 23346 Z= 0.306 Chirality : 0.038 0.329 2850 Planarity : 0.004 0.053 2013 Dihedral : 23.768 169.864 5519 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.83 % Favored : 95.93 % Rotamer: Outliers : 1.96 % Allowed : 13.50 % Favored : 84.54 % 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: -0.12 (0.23), residues: 1227 helix: 0.82 (0.21), residues: 589 sheet: 0.06 (0.51), residues: 109 loop : -1.11 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.000 ARG M 100 TYR 0.018 0.001 TYR M 38 PHE 0.024 0.002 PHE M 71 TRP 0.024 0.002 TRP O 167 HIS 0.005 0.001 HIS O 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (16323) covalent geometry : angle 0.57051 / 0.31 (23346) hydrogen bonds : bond 0.04906 / 3.63 ( 630) hydrogen bonds : angle 4.06166 / 2.84 ( 1666) *********************** 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 85 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 64 ASN cc_start: 0.8109 (m110) cc_final: 0.7530 (m110) outliers start: 21 outliers final: 18 residues processed: 81 average time/residue: 0.1407 time to fit residues: 16.1952 Evaluate side-chains 76 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 72 ARG Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 96 GLN Chi-restraints excluded: chain O residue 167 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 129 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 111 optimal weight: 50.0000 chunk 90 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 11 optimal weight: 0.0000 chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.109891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.088868 restraints weight = 74190.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.088939 restraints weight = 57019.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.089003 restraints weight = 40606.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.089162 restraints weight = 40829.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.089258 restraints weight = 35260.343| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 16323 Z= 0.107 Angle : 0.532 11.050 23346 Z= 0.288 Chirality : 0.036 0.327 2850 Planarity : 0.004 0.052 2013 Dihedral : 23.729 170.511 5519 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.75 % Favored : 96.01 % Rotamer: Outliers : 1.58 % Allowed : 13.87 % Favored : 84.54 % 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: 0.03 (0.24), residues: 1227 helix: 0.98 (0.22), residues: 588 sheet: 0.11 (0.51), residues: 109 loop : -1.08 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 100 TYR 0.016 0.001 TYR M 38 PHE 0.013 0.001 PHE O 172 TRP 0.025 0.002 TRP O 167 HIS 0.006 0.001 HIS O 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (16323) covalent geometry : angle 0.53191 / 0.29 (23346) hydrogen bonds : bond 0.04663 / 3.47 ( 630) hydrogen bonds : angle 3.93782 / 2.75 ( 1666) *********************** 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 76 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 59 LEU cc_start: 0.7823 (tt) cc_final: 0.6920 (mm) REVERT: M 64 ASN cc_start: 0.8225 (m110) cc_final: 0.7550 (m110) outliers start: 17 outliers final: 16 residues processed: 73 average time/residue: 0.1282 time to fit residues: 13.3277 Evaluate side-chains 74 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 938 ARG Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain M residue 96 GLN Chi-restraints excluded: chain O residue 167 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 126 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 104 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 134 optimal weight: 50.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 506 GLN ** 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 = 0.4432 r_free = 0.4432 target = 0.107850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.086192 restraints weight = 73962.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.086313 restraints weight = 50503.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.086473 restraints weight = 38877.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.086254 restraints weight = 34164.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.086505 restraints weight = 32512.693| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.6184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 16323 Z= 0.172 Angle : 0.593 10.717 23346 Z= 0.316 Chirality : 0.039 0.327 2850 Planarity : 0.005 0.053 2013 Dihedral : 23.767 170.083 5519 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.40 % Favored : 95.35 % Rotamer: Outliers : 1.49 % Allowed : 13.97 % Favored : 84.54 % 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: -0.14 (0.23), residues: 1227 helix: 0.84 (0.21), residues: 584 sheet: -0.04 (0.48), residues: 121 loop : -1.14 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 100 TYR 0.016 0.002 TYR M 38 PHE 0.032 0.002 PHE A 693 TRP 0.022 0.002 TRP O 167 HIS 0.007 0.002 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (16323) covalent geometry : angle 0.59327 / 0.32 (23346) hydrogen bonds : bond 0.05187 / 3.88 ( 630) hydrogen bonds : angle 4.15903 / 2.91 ( 1666) ********************** 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 74 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 59 LEU cc_start: 0.7849 (tt) cc_final: 0.6969 (mm) REVERT: M 64 ASN cc_start: 0.8367 (m110) cc_final: 0.7659 (m110) outliers start: 16 outliers final: 14 residues processed: 71 average time/residue: 0.1289 time to fit residues: 13.4006 Evaluate side-chains 69 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain O residue 167 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 144 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 3 optimal weight: 0.0270 chunk 116 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN M 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.109295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.089252 restraints weight = 74395.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.088197 restraints weight = 55193.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.088422 restraints weight = 45784.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.088666 restraints weight = 41456.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.088623 restraints weight = 38196.646| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 16323 Z= 0.111 Angle : 0.541 9.950 23346 Z= 0.291 Chirality : 0.036 0.325 2850 Planarity : 0.005 0.080 2013 Dihedral : 23.760 170.864 5519 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.24 % Favored : 95.52 % Rotamer: Outliers : 1.40 % Allowed : 14.43 % Favored : 84.17 % 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: 0.03 (0.24), residues: 1227 helix: 0.94 (0.21), residues: 587 sheet: 0.10 (0.49), residues: 121 loop : -1.03 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 100 TYR 0.017 0.001 TYR M 38 PHE 0.025 0.001 PHE A 693 TRP 0.023 0.001 TRP O 167 HIS 0.005 0.001 HIS O 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (16323) covalent geometry : angle 0.54129 / 0.29 (23346) hydrogen bonds : bond 0.04653 / 3.45 ( 630) hydrogen bonds : angle 3.95888 / 2.75 ( 1666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2170.39 seconds wall clock time: 38 minutes 15.96 seconds (2295.96 seconds total)