Starting phenix.real_space_refine on Fri Jul 3 19:36:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qaz_52980/07_2026/9qaz_52980.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qaz_52980/07_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_52980/07_2026/9qaz_52980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qaz_52980/07_2026/9qaz_52980.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qaz_52980/07_2026/9qaz_52980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qaz_52980/07_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-dev-6108/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: 2.92, per 1000 atoms: 0.19 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: 0.87 Conformation dependent library (CDL) restraints added in 461.6 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: 1.48 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: 4.14 Time building geometry restraints manager: 1.17 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=" 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 bond pdb=" C2 U B 291 " pdb=" N3 U B 291 " ideal model delta sigma weight residual 1.373 1.394 -0.021 7.00e-03 2.04e+04 8.94e+00 ... (remaining 16318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 22139 2.55 - 5.10: 1157 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 1.50e+00 4.44e-01 7.21e+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=" C4' DG N 29 " pdb=" C3' DG N 29 " pdb=" C2' DG N 29 " ideal model delta sigma weight residual 103.10 99.17 3.93 9.00e-01 1.23e+00 1.91e+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: 2464 0.119 - 0.237: 369 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.100 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.500 ------------------------------------------------------------------------------- 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= 0.597 Angle : 1.228 12.740 23346 Z= 0.838 Chirality : 0.083 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 0.00884 / 0.60 (16323) covalent geometry : angle 1.22846 / 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 : 0.277 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: 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: 0.5609 (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: 0.1463 time to fit residues: 37.7829 Evaluate side-chains 97 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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: 9.9990 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.116257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.097368 restraints weight = 79015.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.097328 restraints weight = 52054.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.097632 restraints weight = 40890.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.097729 restraints weight = 35494.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.097698 restraints weight = 31151.395| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 16323 Z= 0.172 Angle : 0.668 10.505 23346 Z= 0.379 Chirality : 0.041 0.303 2850 Planarity : 0.006 0.097 2013 Dihedral : 24.091 178.474 5519 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 1.49 % Allowed : 6.15 % 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: -1.34 (0.22), residues: 1227 helix: 0.09 (0.20), residues: 575 sheet: -1.78 (0.41), residues: 126 loop : -1.72 (0.24), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 885 TYR 0.016 0.002 TYR A 739 PHE 0.017 0.002 PHE A 544 TRP 0.033 0.003 TRP O 167 HIS 0.008 0.001 HIS O 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (16323) covalent geometry : angle 0.66786 / 0.38 (23346) hydrogen bonds : bond 0.07247 / 5.09 ( 630) hydrogen bonds : angle 4.92784 / 3.56 ( 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 128 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.303 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: 0.6601 (tptt) cc_final: 0.6361 (ttpp) REVERT: O 98 TRP cc_start: 0.6716 (p-90) cc_final: 0.6338 (p-90) outliers start: 16 outliers final: 8 residues processed: 125 average time/residue: 0.1380 time to fit residues: 24.7273 Evaluate side-chains 79 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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: 4.9990 chunk 41 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 135 optimal weight: 30.0000 chunk 60 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.111059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.090725 restraints weight = 76685.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.090663 restraints weight = 57738.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.090495 restraints weight = 44176.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.090680 restraints weight = 42687.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.090726 restraints weight = 38811.840| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 16323 Z= 0.218 Angle : 0.746 14.594 23346 Z= 0.402 Chirality : 0.044 0.284 2850 Planarity : 0.007 0.080 2013 Dihedral : 23.932 174.959 5519 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.83 % Favored : 95.93 % Rotamer: Outliers : 2.14 % Allowed : 8.85 % Favored : 89.01 % 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: -0.98 (0.22), residues: 1227 helix: 0.14 (0.21), residues: 569 sheet: -0.99 (0.45), residues: 119 loop : -1.36 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 787 TYR 0.019 0.002 TYR A 707 PHE 0.032 0.003 PHE A 708 TRP 0.053 0.003 TRP O 167 HIS 0.011 0.002 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.22 (16323) covalent geometry : angle 0.74639 / 0.40 (23346) hydrogen bonds : bond 0.07147 / 5.37 ( 630) hydrogen bonds : angle 4.68144 / 3.40 ( 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 106 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 MET cc_start: 0.1170 (mpp) cc_final: 0.0909 (mpp) REVERT: A 399 ASN cc_start: 0.5096 (m-40) cc_final: 0.4783 (m-40) outliers start: 23 outliers final: 19 residues processed: 104 average time/residue: 0.1287 time to fit residues: 19.4137 Evaluate side-chains 85 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 491 THR 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 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 891 VAL 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 167 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 115 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 140 optimal weight: 30.0000 chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 40.0000 chunk 90 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 HIS ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN A 816 HIS A 879 HIS ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 HIS M 85 ASN M 96 GLN O 122 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.108757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.088558 restraints weight = 75451.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.087486 restraints weight = 57848.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.087546 restraints weight = 49002.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.087686 restraints weight = 45689.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.087768 restraints weight = 38717.608| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16323 Z= 0.216 Angle : 0.676 10.439 23346 Z= 0.372 Chirality : 0.043 0.390 2850 Planarity : 0.006 0.084 2013 Dihedral : 23.976 178.095 5519 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.34 % Favored : 96.33 % Rotamer: Outliers : 3.26 % Allowed : 9.96 % Favored : 86.78 % 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: -0.87 (0.22), residues: 1227 helix: 0.11 (0.20), residues: 576 sheet: -0.55 (0.47), residues: 117 loop : -1.29 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 73 TYR 0.021 0.002 TYR A 894 PHE 0.032 0.003 PHE M 71 TRP 0.019 0.003 TRP O 167 HIS 0.010 0.002 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.22 (16323) covalent geometry : angle 0.67626 / 0.37 (23346) hydrogen bonds : bond 0.05957 / 4.23 ( 630) hydrogen bonds : angle 4.49603 / 3.20 ( 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 102 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 67 time to evaluate : 0.438 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: A 84 VAL cc_start: 0.6823 (OUTLIER) cc_final: 0.6590 (p) REVERT: A 1004 ILE cc_start: 0.8386 (mt) cc_final: 0.8135 (mt) REVERT: L 78 ARG cc_start: 0.7232 (ttt180) cc_final: 0.6757 (tpt-90) outliers start: 35 outliers final: 22 residues processed: 97 average time/residue: 0.1271 time to fit residues: 17.7940 Evaluate side-chains 75 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 839 THR 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 69 ASN Chi-restraints excluded: chain L residue 72 ARG Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain O residue 150 THR Chi-restraints excluded: chain O residue 208 ARG 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: 4.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 GLN A 399 ASN ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.108657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.087703 restraints weight = 75203.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.087140 restraints weight = 55025.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.087056 restraints weight = 48387.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.087255 restraints weight = 45233.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.087339 restraints weight = 40790.959| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16323 Z= 0.164 Angle : 0.594 10.770 23346 Z= 0.328 Chirality : 0.039 0.240 2850 Planarity : 0.005 0.056 2013 Dihedral : 23.924 173.281 5519 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.16 % Favored : 95.60 % Rotamer: Outliers : 2.23 % Allowed : 11.55 % Favored : 86.22 % 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: -0.54 (0.23), residues: 1227 helix: 0.44 (0.21), residues: 573 sheet: -0.54 (0.48), residues: 119 loop : -1.14 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 100 TYR 0.019 0.001 TYR L 51 PHE 0.038 0.002 PHE M 66 TRP 0.027 0.002 TRP O 167 HIS 0.010 0.001 HIS O 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (16323) covalent geometry : angle 0.59364 / 0.33 (23346) hydrogen bonds : bond 0.05476 / 4.06 ( 630) hydrogen bonds : angle 4.30277 / 3.04 ( 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 84 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 VAL cc_start: 0.6805 (OUTLIER) cc_final: 0.6576 (p) REVERT: M 64 ASN cc_start: 0.8340 (m110) cc_final: 0.7698 (m110) REVERT: M 73 ARG cc_start: 0.8000 (mtm110) cc_final: 0.7645 (ptp90) outliers start: 24 outliers final: 17 residues processed: 79 average time/residue: 0.1233 time to fit residues: 14.3525 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 : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 384 GLN Chi-restraints excluded: chain A residue 408 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 617 LEU Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 839 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 M residue 40 VAL Chi-restraints excluded: chain O residue 150 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 137 optimal weight: 0.1980 chunk 75 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 135 optimal weight: 40.0000 chunk 7 optimal weight: 0.8980 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 = 0.4437 r_free = 0.4437 target = 0.108343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.087439 restraints weight = 75039.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.087572 restraints weight = 54569.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.087645 restraints weight = 43605.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.087719 restraints weight = 38706.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.087729 restraints weight = 35392.050| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16323 Z= 0.155 Angle : 0.575 8.491 23346 Z= 0.318 Chirality : 0.038 0.228 2850 Planarity : 0.005 0.056 2013 Dihedral : 23.887 171.824 5519 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.83 % Favored : 95.93 % Rotamer: Outliers : 2.61 % Allowed : 11.64 % Favored : 85.75 % 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: -0.45 (0.23), residues: 1227 helix: 0.53 (0.21), residues: 581 sheet: -0.40 (0.48), residues: 119 loop : -1.15 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 385 TYR 0.012 0.001 TYR M 38 PHE 0.022 0.002 PHE M 66 TRP 0.014 0.002 TRP O 167 HIS 0.007 0.001 HIS O 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (16323) covalent geometry : angle 0.57549 / 0.32 (23346) hydrogen bonds : bond 0.05147 / 3.79 ( 630) hydrogen bonds : angle 4.19480 / 2.94 ( 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 89 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6271 (tp) REVERT: A 852 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7654 (ptpt) REVERT: L 78 ARG cc_start: 0.7333 (ttt180) cc_final: 0.7115 (tpt-90) REVERT: M 64 ASN cc_start: 0.8085 (m110) cc_final: 0.7400 (m110) outliers start: 28 outliers final: 21 residues processed: 85 average time/residue: 0.1134 time to fit residues: 14.3419 Evaluate side-chains 78 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 874 THR 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 69 ASN Chi-restraints excluded: chain M residue 40 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 12 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.107325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.086669 restraints weight = 74310.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.085788 restraints weight = 55640.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.085921 restraints weight = 47873.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.086145 restraints weight = 42858.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.086173 restraints weight = 37573.242| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.5988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16323 Z= 0.171 Angle : 0.588 9.502 23346 Z= 0.323 Chirality : 0.039 0.352 2850 Planarity : 0.006 0.121 2013 Dihedral : 23.911 170.333 5519 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.56 % Favored : 95.19 % Rotamer: Outliers : 2.42 % Allowed : 12.85 % Favored : 84.73 % 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: -0.44 (0.23), residues: 1227 helix: 0.49 (0.21), residues: 581 sheet: -0.23 (0.48), residues: 119 loop : -1.14 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG M 73 TYR 0.014 0.001 TYR A 739 PHE 0.035 0.002 PHE M 71 TRP 0.016 0.002 TRP A 510 HIS 0.006 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (16323) covalent geometry : angle 0.58810 / 0.32 (23346) hydrogen bonds : bond 0.05271 / 3.91 ( 630) hydrogen bonds : angle 4.26717 / 3.00 ( 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 88 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6705 (tp) REVERT: L 78 ARG cc_start: 0.7456 (ttt180) cc_final: 0.7203 (tpt-90) outliers start: 26 outliers final: 19 residues processed: 85 average time/residue: 0.1268 time to fit residues: 15.5385 Evaluate side-chains 77 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 556 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 835 SER Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 891 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 69 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 121 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 = 0.4436 r_free = 0.4436 target = 0.108089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.087181 restraints weight = 75075.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.087499 restraints weight = 55413.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.087595 restraints weight = 40717.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.087440 restraints weight = 36449.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.087543 restraints weight = 34717.602| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.6148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16323 Z= 0.123 Angle : 0.531 10.057 23346 Z= 0.295 Chirality : 0.036 0.218 2850 Planarity : 0.005 0.054 2013 Dihedral : 23.875 169.237 5519 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.67 % Favored : 96.09 % 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: -0.26 (0.23), residues: 1227 helix: 0.71 (0.21), residues: 587 sheet: -0.08 (0.48), residues: 121 loop : -1.19 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 208 TYR 0.011 0.001 TYR A 739 PHE 0.024 0.002 PHE M 71 TRP 0.011 0.001 TRP A 547 HIS 0.008 0.001 HIS O 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (16323) covalent geometry : angle 0.53104 / 0.30 (23346) hydrogen bonds : bond 0.04713 / 3.48 ( 630) hydrogen bonds : angle 4.09026 / 2.86 ( 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 76 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6484 (tp) REVERT: A 773 MET cc_start: 0.8299 (tpt) cc_final: 0.7935 (tpt) REVERT: L 78 ARG cc_start: 0.7512 (ttt180) cc_final: 0.7294 (tpt-90) outliers start: 16 outliers final: 14 residues processed: 74 average time/residue: 0.1325 time to fit residues: 13.9788 Evaluate side-chains 72 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 556 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 718 ASP Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1016 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 129 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 111 optimal weight: 40.0000 chunk 90 optimal weight: 4.9990 chunk 100 optimal weight: 30.0000 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1022 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.104794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.083415 restraints weight = 74100.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.083327 restraints weight = 58452.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.083705 restraints weight = 42947.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.083714 restraints weight = 39658.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.083740 restraints weight = 37324.354| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.6879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16323 Z= 0.260 Angle : 0.717 9.306 23346 Z= 0.386 Chirality : 0.044 0.327 2850 Planarity : 0.006 0.068 2013 Dihedral : 24.128 168.669 5519 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.46 % Favored : 94.30 % Rotamer: Outliers : 2.14 % Allowed : 13.31 % 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: -0.81 (0.23), residues: 1227 helix: 0.14 (0.20), residues: 585 sheet: -0.16 (0.47), residues: 128 loop : -1.36 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 208 TYR 0.020 0.002 TYR A 168 PHE 0.031 0.003 PHE A 27 TRP 0.021 0.002 TRP A 478 HIS 0.008 0.002 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.26 (16323) covalent geometry : angle 0.71693 / 0.39 (23346) hydrogen bonds : bond 0.06655 / 4.85 ( 630) hydrogen bonds : angle 4.78782 / 3.36 ( 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 85 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6587 (tp) REVERT: A 787 ARG cc_start: 0.5001 (mmp80) cc_final: 0.4592 (mmp80) REVERT: L 78 ARG cc_start: 0.7749 (ttt180) cc_final: 0.7317 (tpt-90) outliers start: 23 outliers final: 16 residues processed: 83 average time/residue: 0.1418 time to fit residues: 17.0692 Evaluate side-chains 75 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 556 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 835 SER Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1016 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 M residue 42 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 126 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS ** M 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.107105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.085890 restraints weight = 74822.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.085947 restraints weight = 52667.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.086061 restraints weight = 44058.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.086034 restraints weight = 37043.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.086149 restraints weight = 36436.329| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.6911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16323 Z= 0.131 Angle : 0.577 11.460 23346 Z= 0.319 Chirality : 0.038 0.233 2850 Planarity : 0.005 0.052 2013 Dihedral : 24.052 169.098 5519 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.83 % Favored : 95.93 % Rotamer: Outliers : 1.30 % Allowed : 14.62 % Favored : 84.08 % 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: -0.43 (0.23), residues: 1227 helix: 0.50 (0.21), residues: 585 sheet: -0.09 (0.47), residues: 129 loop : -1.20 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 73 TYR 0.019 0.001 TYR A 562 PHE 0.033 0.002 PHE M 71 TRP 0.032 0.002 TRP A 581 HIS 0.006 0.001 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (16323) covalent geometry : angle 0.57720 / 0.32 (23346) hydrogen bonds : bond 0.04951 / 3.63 ( 630) hydrogen bonds : angle 4.29158 / 3.01 ( 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 75 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6751 (tp) REVERT: L 78 ARG cc_start: 0.7567 (ttt180) cc_final: 0.7118 (tpt-90) outliers start: 14 outliers final: 11 residues processed: 72 average time/residue: 0.1377 time to fit residues: 14.2951 Evaluate side-chains 71 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 408 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 891 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 69 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 144 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 47 optimal weight: 0.3980 chunk 114 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 0.0370 overall best weight: 1.0460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN ** A 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.107916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.087343 restraints weight = 74556.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.086796 restraints weight = 57630.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.086738 restraints weight = 44658.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.086928 restraints weight = 43376.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.086955 restraints weight = 38939.511| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.7046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16323 Z= 0.119 Angle : 0.540 9.823 23346 Z= 0.298 Chirality : 0.037 0.321 2850 Planarity : 0.005 0.050 2013 Dihedral : 23.913 170.745 5519 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.40 % Favored : 95.35 % Rotamer: Outliers : 1.21 % Allowed : 15.08 % Favored : 83.71 % 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: -0.10 (0.24), residues: 1227 helix: 0.81 (0.21), residues: 585 sheet: -0.16 (0.47), residues: 135 loop : -1.03 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG M 73 TYR 0.022 0.001 TYR M 38 PHE 0.011 0.001 PHE A 693 TRP 0.015 0.002 TRP A 510 HIS 0.007 0.001 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (16323) covalent geometry : angle 0.54029 / 0.30 (23346) hydrogen bonds : bond 0.04682 / 3.49 ( 630) hydrogen bonds : angle 4.08164 / 2.85 ( 1666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2188.54 seconds wall clock time: 38 minutes 42.41 seconds (2322.41 seconds total)