Starting phenix.real_space_refine on Fri Jul 3 19:38:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qay_52979/07_2026/9qay_52979.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qay_52979/07_2026/9qay_52979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qay_52979/07_2026/9qay_52979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qay_52979/07_2026/9qay_52979.map" model { file = "/net/cci-nas-00/data/ceres_data/9qay_52979/07_2026/9qay_52979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qay_52979/07_2026/9qay_52979.cif" } resolution = 3.8 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 123 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': 16, 'rna2p_pyr': 18, 'rna3p_pur': 100, 'rna3p_pyr': 119} Link IDs: {'rna2p': 34, 'rna3p': 218} 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: 3.25, per 1000 atoms: 0.21 Number of scatterers: 15471 At special positions: 0 Unit cell: (167.322, 124.962, 144.024, 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: 0.99 Conformation dependent library (CDL) restraints added in 490.0 milliseconds 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2346 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 9 sheets defined 54.3% alpha, 12.7% beta 71 base pairs and 125 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 removed outlier: 3.899A 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: 3.584A pdb=" N VAL A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 92 removed outlier: 3.579A pdb=" N VAL A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 removed outlier: 3.853A 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: 3.701A pdb=" N ARG A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.732A pdb=" N LEU A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 353 through 366 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 389 through 402 removed outlier: 3.657A pdb=" N PHE A 393 " --> pdb=" O MET A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.504A pdb=" N LEU A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 454 removed outlier: 3.516A pdb=" N ARG A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 473 removed outlier: 3.923A pdb=" N ARG A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.692A 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: 3.676A pdb=" N LEU A 520 " --> pdb=" O CYS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 551 removed outlier: 3.508A pdb=" N LYS A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 removed outlier: 3.611A pdb=" N PHE A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 597 removed outlier: 3.711A pdb=" N LYS A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 596 " --> pdb=" O HIS A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.665A pdb=" N GLU A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 672 removed outlier: 4.097A 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: 3.854A pdb=" N THR A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 734 removed outlier: 3.665A pdb=" N GLU A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 733 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 769 removed outlier: 3.581A 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: 3.640A pdb=" N CYS A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 843 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 3.615A 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: 3.693A pdb=" N ALA A 880 " --> pdb=" O HIS A 876 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 890 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 950 removed outlier: 3.619A pdb=" N TYR A 949 " --> pdb=" O TYR A 946 " (cutoff:3.500A) removed outlier: 3.509A 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: 3.557A 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: 3.562A pdb=" N LEU A1007 " --> pdb=" O LYS A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1028 removed outlier: 3.538A pdb=" N LYS A1027 " --> pdb=" O GLN A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1051 removed outlier: 3.546A pdb=" N ASP A1038 " --> pdb=" O ARG A1034 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A1043 " --> pdb=" O THR A1039 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1085 removed outlier: 3.902A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.719A 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: 3.822A pdb=" N ARG A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) removed outlier: 3.965A 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: 4.090A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A1106 " --> pdb=" O GLN A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1119 removed outlier: 3.879A pdb=" N THR A1113 " --> pdb=" O GLY A1109 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 38 removed outlier: 4.411A 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: 3.572A pdb=" N GLY L 38 " --> pdb=" O LEU L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 73 removed outlier: 4.507A pdb=" N VAL L 50 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR L 51 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU L 57 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU L 66 " --> pdb=" O GLU L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 91 removed outlier: 3.965A pdb=" N LEU L 84 " --> pdb=" O ILE L 80 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP L 91 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 99 removed outlier: 3.636A 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: 3.629A pdb=" N VAL M 45 " --> pdb=" O TYR M 41 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS M 47 " --> pdb=" O TYR M 43 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN M 48 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL M 49 " --> pdb=" O VAL M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 86 removed outlier: 4.001A pdb=" N SER M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE M 66 " --> pdb=" O ILE M 62 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE M 70 " --> pdb=" O PHE M 66 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS M 83 " --> pdb=" O SER M 79 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR M 84 " --> pdb=" O ARG M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 103 removed outlier: 3.781A 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: 5.166A pdb=" N THR M 97 " --> pdb=" O ARG M 93 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALA M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG M 100 " --> pdb=" O GLN M 96 " (cutoff:3.500A) removed outlier: 3.696A 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: 3.684A pdb=" N GLU M 114 " --> pdb=" O HIS M 110 " (cutoff:3.500A) removed outlier: 4.232A 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: 3.721A pdb=" N SER M 125 " --> pdb=" O LYS M 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 104 removed outlier: 3.842A 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: 3.505A 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: 3.908A 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: 4.435A 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: 3.771A pdb=" N ALA A 157 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.642A 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: 3.771A pdb=" N ALA A 157 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.642A 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: 3.530A 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: 7.355A pdb=" N LEU A 617 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ARG A 819 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.348A 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: 3.717A pdb=" N LEU A 866 " --> pdb=" O ASP A 869 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A 869 " --> pdb=" O LEU A 866 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 711 " --> pdb=" O PHE A 870 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 709 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 3.536A 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: 5.663A pdb=" N VAL O 120 " --> pdb=" O THR O 143 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR O 143 " --> pdb=" O VAL O 120 " (cutoff:3.500A) removed outlier: 9.521A 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) 458 hydrogen bonds defined for protein. 1326 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: 4.30 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1962 1.32 - 1.45: 5806 1.45 - 1.57: 7985 1.57 - 1.70: 515 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 1.191 0.043 1.06e-02 8.90e+03 1.64e+01 bond pdb=" C VAL A 563 " pdb=" O VAL A 563 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.20e-02 6.94e+03 1.32e+01 bond pdb=" CZ ARG L 33 " pdb=" NH2 ARG L 33 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.14e+01 bond pdb=" C4 C B 313 " pdb=" C5 C B 313 " ideal model delta sigma weight residual 1.425 1.450 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" O5' DG N 28 " pdb=" C5' DG N 28 " ideal model delta sigma weight residual 1.418 1.496 -0.078 2.50e-02 1.60e+03 9.86e+00 ... (remaining 16318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 22186 2.57 - 5.14: 1111 5.14 - 7.71: 41 7.71 - 10.29: 4 10.29 - 12.86: 4 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 91.14 12.86 1.50e+00 4.44e-01 7.35e+01 angle pdb=" O6 G B 58 " pdb=" C6 G B 58 " pdb=" N1 G B 58 " ideal model delta sigma weight residual 119.90 116.20 3.70 6.00e-01 2.78e+00 3.80e+01 angle pdb=" C LYS A 338 " pdb=" CA LYS A 338 " pdb=" CB LYS A 338 " ideal model delta sigma weight residual 109.84 101.62 8.22 1.50e+00 4.44e-01 3.00e+01 angle pdb=" C HIS A1022 " pdb=" CA HIS A1022 " pdb=" CB HIS A1022 " ideal model delta sigma weight residual 110.42 121.08 -10.66 1.99e+00 2.53e-01 2.87e+01 angle pdb=" N PRO A 530 " pdb=" CA PRO A 530 " pdb=" C PRO A 530 " ideal model delta sigma weight residual 110.40 117.67 -7.27 1.61e+00 3.86e-01 2.04e+01 ... (remaining 23341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 9448 35.74 - 71.48: 707 71.48 - 107.22: 110 107.22 - 142.96: 7 142.96 - 178.70: 12 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 74.41 72.59 1 8.00e+00 1.56e-02 1.05e+02 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 35.36 -70.36 1 8.00e+00 1.56e-02 9.96e+01 dihedral pdb=" C4' A B 176 " pdb=" C3' A B 176 " pdb=" C2' A B 176 " pdb=" C1' A B 176 " ideal model delta sinusoidal sigma weight residual -35.00 33.60 -68.60 1 8.00e+00 1.56e-02 9.53e+01 ... (remaining 10281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2502 0.119 - 0.238: 330 0.238 - 0.357: 13 0.357 - 0.476: 1 0.476 - 0.595: 4 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 8.85e+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 6.79e+00 chirality pdb=" P DG N 28 " pdb=" OP1 DG N 28 " pdb=" OP2 DG N 28 " pdb=" O5' DG N 28 " both_signs ideal model delta sigma weight residual True 2.34 -2.85 -0.51 2.00e-01 2.50e+01 6.56e+00 ... (remaining 2847 not shown) Planarity restraints: 2013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 142 " -0.208 2.00e-02 2.50e+03 1.05e-01 2.50e+02 pdb=" N1 C B 142 " 0.051 2.00e-02 2.50e+03 pdb=" C2 C B 142 " 0.057 2.00e-02 2.50e+03 pdb=" O2 C B 142 " 0.055 2.00e-02 2.50e+03 pdb=" N3 C B 142 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C B 142 " 0.055 2.00e-02 2.50e+03 pdb=" N4 C B 142 " -0.176 2.00e-02 2.50e+03 pdb=" C5 C B 142 " 0.067 2.00e-02 2.50e+03 pdb=" C6 C B 142 " 0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 307 " -0.105 2.00e-02 2.50e+03 5.73e-02 7.38e+01 pdb=" N1 U B 307 " 0.091 2.00e-02 2.50e+03 pdb=" C2 U B 307 " 0.010 2.00e-02 2.50e+03 pdb=" O2 U B 307 " 0.052 2.00e-02 2.50e+03 pdb=" N3 U B 307 " -0.053 2.00e-02 2.50e+03 pdb=" C4 U B 307 " -0.022 2.00e-02 2.50e+03 pdb=" O4 U B 307 " -0.027 2.00e-02 2.50e+03 pdb=" C5 U B 307 " 0.059 2.00e-02 2.50e+03 pdb=" C6 U B 307 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 690 " -0.086 2.00e-02 2.50e+03 4.81e-02 5.78e+01 pdb=" CG TRP A 690 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 690 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 690 " 0.076 2.00e-02 2.50e+03 pdb=" NE1 TRP A 690 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 690 " 0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP A 690 " 0.056 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 690 " -0.022 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 690 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 690 " -0.065 2.00e-02 2.50e+03 ... (remaining 2010 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.00: 3 2.00 - 2.73: 882 2.73 - 3.45: 20308 3.45 - 4.18: 39930 4.18 - 4.90: 61174 Nonbonded interactions: 122297 Sorted by model distance: nonbonded pdb=" O TRP A 510 " pdb=" O2' C B 313 " model vdw 1.280 3.040 nonbonded pdb=" CA HIS A 752 " pdb=" O6 G B 58 " model vdw 1.833 3.470 nonbonded pdb=" OG SER A 12 " pdb=" O2' A B 61 " model vdw 1.833 3.040 nonbonded pdb=" C HIS A 752 " pdb=" O6 G B 58 " model vdw 2.006 3.270 nonbonded pdb=" O PHE A1021 " pdb=" O2' U B 312 " model vdw 2.033 3.040 ... (remaining 122292 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.980 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 0.091 16323 Z= 0.591 Angle : 1.226 12.857 23346 Z= 0.838 Chirality : 0.082 0.595 2850 Planarity : 0.012 0.166 2013 Dihedral : 21.975 178.697 7938 Min Nonbonded Distance : 1.280 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.19 % Favored : 93.40 % Rotamer: Outliers : 0.09 % Allowed : 1.96 % Favored : 97.95 % Cbeta Deviations : 0.17 % 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: -3.03 (0.19), residues: 1227 helix: -1.77 (0.17), residues: 535 sheet: -1.92 (0.43), residues: 106 loop : -2.20 (0.22), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.003 ARG A 470 TYR 0.041 0.008 TYR A 946 PHE 0.043 0.008 PHE A 986 TRP 0.086 0.011 TRP A 690 HIS 0.019 0.004 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00874 / 0.59 (16323) covalent geometry : angle 1.22636 / 0.84 (23346) hydrogen bonds : bond 0.27776 / 18.77 ( 632) hydrogen bonds : angle 8.37247 / 5.94 ( 1672) *********************** 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 178 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.483 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: symmetry clash REVERT: A 178 LEU cc_start: 0.7258 (mt) cc_final: 0.7046 (mp) REVERT: A 337 ASP cc_start: 0.8904 (m-30) cc_final: 0.8091 (t0) REVERT: A 512 MET cc_start: 0.7802 (mmt) cc_final: 0.7568 (mmm) REVERT: A 709 VAL cc_start: 0.7825 (t) cc_final: 0.7211 (p) REVERT: A 718 ASP cc_start: 0.8359 (t70) cc_final: 0.8126 (t0) REVERT: A 739 TYR cc_start: 0.6747 (m-80) cc_final: 0.6541 (m-80) REVERT: A 782 GLU cc_start: 0.9286 (tt0) cc_final: 0.9077 (pt0) REVERT: A 799 ASN cc_start: 0.7797 (t0) cc_final: 0.7434 (m110) REVERT: A 824 SER cc_start: 0.8934 (m) cc_final: 0.8709 (p) REVERT: A 860 ASP cc_start: 0.7974 (m-30) cc_final: 0.7220 (p0) REVERT: A 942 VAL cc_start: 0.8171 (t) cc_final: 0.7967 (p) REVERT: A 1054 MET cc_start: 0.6568 (mtt) cc_final: 0.6301 (mtt) REVERT: L 52 LEU cc_start: 0.8141 (tt) cc_final: 0.7721 (pp) REVERT: L 63 ILE cc_start: 0.7011 (tt) cc_final: 0.6653 (tp) REVERT: L 74 ASN cc_start: 0.7583 (t0) cc_final: 0.7197 (m110) REVERT: M 62 ILE cc_start: 0.8092 (mm) cc_final: 0.7629 (mm) REVERT: O 148 ASP cc_start: 0.4296 (p0) cc_final: 0.3792 (p0) REVERT: O 174 PHE cc_start: 0.6027 (m-80) cc_final: 0.5725 (m-10) REVERT: O 209 PHE cc_start: 0.8176 (p90) cc_final: 0.7769 (p90) REVERT: O 218 ARG cc_start: 0.7990 (mtm180) cc_final: 0.7729 (mtm-85) outliers start: 1 outliers final: 1 residues processed: 177 average time/residue: 0.1735 time to fit residues: 41.8741 Evaluate side-chains 104 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 40 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 40.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 460 GLN A1102 GLN L 85 GLN M 50 HIS ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 151 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.113831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.089955 restraints weight = 83930.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.091628 restraints weight = 41901.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.092766 restraints weight = 28241.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.093013 restraints weight = 22983.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.093640 restraints weight = 21397.125| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16323 Z= 0.175 Angle : 0.666 10.897 23346 Z= 0.373 Chirality : 0.040 0.272 2850 Planarity : 0.006 0.078 2013 Dihedral : 24.056 178.938 5520 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.25 % Rotamer: Outliers : 1.40 % Allowed : 7.91 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.21), residues: 1227 helix: -0.09 (0.20), residues: 573 sheet: -1.73 (0.40), residues: 119 loop : -1.74 (0.23), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 92 TYR 0.012 0.002 TYR M 122 PHE 0.037 0.002 PHE M 66 TRP 0.021 0.003 TRP A 547 HIS 0.012 0.001 HIS A 925 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (16323) covalent geometry : angle 0.66550 / 0.37 (23346) hydrogen bonds : bond 0.07813 / 5.29 ( 632) hydrogen bonds : angle 4.95667 / 3.61 ( 1672) *********************** 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 131 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7494 (mt) cc_final: 0.7288 (mp) REVERT: A 363 THR cc_start: 0.7373 (m) cc_final: 0.6616 (p) REVERT: A 472 LEU cc_start: 0.8734 (tp) cc_final: 0.8450 (tp) REVERT: A 536 LEU cc_start: 0.8554 (tp) cc_final: 0.8300 (tt) REVERT: A 739 TYR cc_start: 0.4796 (m-80) cc_final: 0.4542 (m-80) REVERT: A 824 SER cc_start: 0.7248 (m) cc_final: 0.6973 (p) REVERT: M 62 ILE cc_start: 0.8112 (mm) cc_final: 0.7800 (mm) REVERT: M 63 MET cc_start: 0.9492 (OUTLIER) cc_final: 0.9264 (mpp) REVERT: M 66 PHE cc_start: 0.8644 (m-80) cc_final: 0.8361 (m-80) REVERT: O 98 TRP cc_start: 0.4481 (p-90) cc_final: 0.4044 (p-90) outliers start: 15 outliers final: 8 residues processed: 126 average time/residue: 0.1459 time to fit residues: 26.0151 Evaluate side-chains 93 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 26 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 141 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 GLN A 983 HIS A1018 GLN O 151 HIS O 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.105279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.081274 restraints weight = 81477.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.081463 restraints weight = 46713.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.081906 restraints weight = 34119.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.082301 restraints weight = 28231.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.082293 restraints weight = 27012.069| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 16323 Z= 0.300 Angle : 0.818 9.822 23346 Z= 0.449 Chirality : 0.048 0.271 2850 Planarity : 0.008 0.116 2013 Dihedral : 24.196 179.909 5520 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.27 % Rotamer: Outliers : 2.61 % Allowed : 9.68 % Favored : 87.71 % 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: -1.44 (0.21), residues: 1227 helix: -0.30 (0.20), residues: 577 sheet: -1.24 (0.44), residues: 116 loop : -1.53 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG O 92 TYR 0.026 0.003 TYR A 576 PHE 0.027 0.003 PHE A 623 TRP 0.021 0.003 TRP A 930 HIS 0.015 0.002 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.30 (16323) covalent geometry : angle 0.81839 / 0.45 (23346) hydrogen bonds : bond 0.09257 / 6.49 ( 632) hydrogen bonds : angle 5.13051 / 3.75 ( 1672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7813 (mt) cc_final: 0.7537 (mp) REVERT: A 860 ASP cc_start: 0.5525 (OUTLIER) cc_final: 0.4837 (p0) REVERT: A 876 HIS cc_start: 0.7336 (m90) cc_final: 0.7087 (m90) REVERT: A 1038 ASP cc_start: 0.8122 (m-30) cc_final: 0.7729 (m-30) REVERT: M 62 ILE cc_start: 0.7950 (mm) cc_final: 0.7504 (mm) REVERT: M 63 MET cc_start: 0.9374 (OUTLIER) cc_final: 0.8895 (mpp) REVERT: M 66 PHE cc_start: 0.8798 (m-80) cc_final: 0.8294 (m-80) REVERT: O 97 PRO cc_start: 0.8069 (Cg_endo) cc_final: 0.7828 (Cg_exo) REVERT: O 98 TRP cc_start: 0.5041 (p-90) cc_final: 0.4055 (p-90) outliers start: 28 outliers final: 16 residues processed: 112 average time/residue: 0.1245 time to fit residues: 20.3229 Evaluate side-chains 86 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 860 ASP 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 1037 SER Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 115 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 140 optimal weight: 40.0000 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 30.0000 chunk 90 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 96 GLN O 151 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.106688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.082736 restraints weight = 80772.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.083337 restraints weight = 44792.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.083661 restraints weight = 32574.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.084165 restraints weight = 26191.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.084058 restraints weight = 24711.838| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16323 Z= 0.167 Angle : 0.605 12.382 23346 Z= 0.337 Chirality : 0.040 0.249 2850 Planarity : 0.005 0.052 2013 Dihedral : 24.190 179.484 5520 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.93 % Favored : 96.90 % Rotamer: Outliers : 2.33 % Allowed : 11.45 % 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: -0.91 (0.22), residues: 1227 helix: 0.24 (0.20), residues: 575 sheet: -1.00 (0.46), residues: 116 loop : -1.39 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 73 TYR 0.012 0.002 TYR A 552 PHE 0.025 0.002 PHE O 209 TRP 0.014 0.002 TRP A1026 HIS 0.006 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (16323) covalent geometry : angle 0.60462 / 0.34 (23346) hydrogen bonds : bond 0.06333 / 4.44 ( 632) hydrogen bonds : angle 4.55793 / 3.35 ( 1672) *********************** 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 104 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8830 (mt) cc_final: 0.8530 (mt) REVERT: A 178 LEU cc_start: 0.7767 (mt) cc_final: 0.7498 (mp) REVERT: A 512 MET cc_start: 0.8721 (mmm) cc_final: 0.8425 (mmm) REVERT: A 1038 ASP cc_start: 0.8150 (m-30) cc_final: 0.7792 (m-30) REVERT: L 74 ASN cc_start: 0.7675 (t0) cc_final: 0.7050 (m110) REVERT: M 62 ILE cc_start: 0.7927 (mm) cc_final: 0.7105 (mt) REVERT: M 63 MET cc_start: 0.9394 (mpp) cc_final: 0.8891 (mpp) REVERT: M 66 PHE cc_start: 0.8800 (m-80) cc_final: 0.8272 (m-80) REVERT: O 97 PRO cc_start: 0.8085 (Cg_endo) cc_final: 0.7806 (Cg_exo) REVERT: O 98 TRP cc_start: 0.5261 (p-90) cc_final: 0.4211 (p-90) REVERT: O 203 TYR cc_start: 0.7607 (p90) cc_final: 0.7372 (p90) REVERT: O 215 GLU cc_start: 0.6030 (pm20) cc_final: 0.5729 (pm20) outliers start: 25 outliers final: 18 residues processed: 99 average time/residue: 0.1014 time to fit residues: 15.5052 Evaluate side-chains 92 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain O residue 116 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 105 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 114 optimal weight: 10.9990 chunk 47 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN A 609 HIS A 969 ASN O 151 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.105749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.081287 restraints weight = 80244.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.081905 restraints weight = 45167.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.082368 restraints weight = 32650.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.082499 restraints weight = 27450.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.082503 restraints weight = 25405.963| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16323 Z= 0.162 Angle : 0.581 8.710 23346 Z= 0.323 Chirality : 0.039 0.243 2850 Planarity : 0.005 0.057 2013 Dihedral : 24.113 174.819 5520 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.99 % Favored : 95.84 % Rotamer: Outliers : 2.51 % Allowed : 11.82 % Favored : 85.66 % 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: -0.58 (0.23), residues: 1227 helix: 0.45 (0.21), residues: 579 sheet: -0.54 (0.49), residues: 114 loop : -1.24 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 865 TYR 0.023 0.002 TYR A 552 PHE 0.020 0.002 PHE A 544 TRP 0.007 0.001 TRP A 581 HIS 0.007 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (16323) covalent geometry : angle 0.58143 / 0.32 (23346) hydrogen bonds : bond 0.06212 / 4.20 ( 632) hydrogen bonds : angle 4.43881 / 3.27 ( 1672) *********************** 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 107 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8808 (mt) cc_final: 0.8574 (mt) REVERT: A 512 MET cc_start: 0.8775 (mmm) cc_final: 0.8548 (mmm) REVERT: A 849 MET cc_start: 0.7305 (ttp) cc_final: 0.6870 (ttp) REVERT: A 969 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8093 (t0) REVERT: A 1038 ASP cc_start: 0.8142 (m-30) cc_final: 0.7764 (m-30) REVERT: M 62 ILE cc_start: 0.7881 (mm) cc_final: 0.6856 (mt) REVERT: M 63 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.8878 (mpp) REVERT: M 66 PHE cc_start: 0.8916 (m-10) cc_final: 0.8253 (m-80) REVERT: O 97 PRO cc_start: 0.8077 (Cg_endo) cc_final: 0.7844 (Cg_exo) REVERT: O 98 TRP cc_start: 0.5474 (p-90) cc_final: 0.4162 (p-90) REVERT: O 203 TYR cc_start: 0.7660 (p90) cc_final: 0.7439 (p90) outliers start: 27 outliers final: 19 residues processed: 99 average time/residue: 0.1011 time to fit residues: 15.7294 Evaluate side-chains 94 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1054 MET Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 MET Chi-restraints excluded: chain O residue 116 GLN 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: 0.5980 chunk 58 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 135 optimal weight: 0.0030 chunk 7 optimal weight: 8.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 151 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.106802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.082399 restraints weight = 80325.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.082618 restraints weight = 45067.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.083342 restraints weight = 34788.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.084360 restraints weight = 26120.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.084133 restraints weight = 24183.418| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16323 Z= 0.120 Angle : 0.529 8.139 23346 Z= 0.297 Chirality : 0.037 0.214 2850 Planarity : 0.004 0.049 2013 Dihedral : 24.063 174.142 5520 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.02 % Favored : 96.82 % Rotamer: Outliers : 1.96 % Allowed : 13.13 % Favored : 84.92 % 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: -0.27 (0.23), residues: 1227 helix: 0.72 (0.21), residues: 576 sheet: -0.71 (0.48), residues: 125 loop : -1.00 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 32 TYR 0.017 0.001 TYR A 168 PHE 0.014 0.001 PHE O 174 TRP 0.009 0.001 TRP A 547 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (16323) covalent geometry : angle 0.52886 / 0.30 (23346) hydrogen bonds : bond 0.05328 / 3.58 ( 632) hydrogen bonds : angle 4.26782 / 3.13 ( 1672) *********************** 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 97 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 739 TYR cc_start: 0.5227 (m-80) cc_final: 0.4970 (m-80) REVERT: A 873 VAL cc_start: 0.7231 (OUTLIER) cc_final: 0.6966 (t) REVERT: A 1038 ASP cc_start: 0.8131 (m-30) cc_final: 0.7749 (m-30) REVERT: M 62 ILE cc_start: 0.7763 (mm) cc_final: 0.7031 (mm) REVERT: M 63 MET cc_start: 0.9402 (OUTLIER) cc_final: 0.8959 (mpp) REVERT: M 66 PHE cc_start: 0.8768 (m-10) cc_final: 0.8176 (m-80) REVERT: M 73 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.7748 (mmp80) REVERT: O 97 PRO cc_start: 0.8164 (Cg_endo) cc_final: 0.7902 (Cg_exo) REVERT: O 98 TRP cc_start: 0.5685 (p-90) cc_final: 0.4339 (p-90) REVERT: O 215 GLU cc_start: 0.6894 (pm20) cc_final: 0.6649 (pm20) outliers start: 21 outliers final: 13 residues processed: 90 average time/residue: 0.1121 time to fit residues: 16.0528 Evaluate side-chains 87 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1015 CYS Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1054 MET Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 MET Chi-restraints excluded: chain O residue 116 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 12 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 5 optimal weight: 0.0870 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.3160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 151 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.106517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.082118 restraints weight = 80258.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.082412 restraints weight = 44568.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.083065 restraints weight = 34298.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.083115 restraints weight = 26742.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.083298 restraints weight = 25267.080| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16323 Z= 0.125 Angle : 0.535 10.453 23346 Z= 0.295 Chirality : 0.037 0.211 2850 Planarity : 0.004 0.048 2013 Dihedral : 23.977 174.571 5520 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.67 % Favored : 96.25 % Rotamer: Outliers : 1.96 % Allowed : 13.78 % Favored : 84.26 % 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: -0.02 (0.23), residues: 1227 helix: 0.95 (0.21), residues: 576 sheet: -0.68 (0.47), residues: 127 loop : -0.87 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 6 TYR 0.018 0.001 TYR A 638 PHE 0.012 0.001 PHE A 494 TRP 0.008 0.001 TRP A 371 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (16323) covalent geometry : angle 0.53502 / 0.29 (23346) hydrogen bonds : bond 0.05192 / 3.47 ( 632) hydrogen bonds : angle 4.17592 / 3.05 ( 1672) *********************** 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 97 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 LEU cc_start: 0.9491 (tp) cc_final: 0.9184 (tt) REVERT: A 849 MET cc_start: 0.7377 (ttp) cc_final: 0.7152 (tmm) REVERT: A 873 VAL cc_start: 0.7319 (OUTLIER) cc_final: 0.7088 (t) REVERT: A 1038 ASP cc_start: 0.8076 (m-30) cc_final: 0.7665 (m-30) REVERT: M 62 ILE cc_start: 0.7717 (mm) cc_final: 0.6936 (mm) REVERT: M 63 MET cc_start: 0.9370 (OUTLIER) cc_final: 0.8910 (mpp) REVERT: M 66 PHE cc_start: 0.8774 (m-10) cc_final: 0.8162 (m-80) REVERT: M 73 ARG cc_start: 0.8432 (mmm-85) cc_final: 0.7753 (mmm160) REVERT: O 97 PRO cc_start: 0.8190 (Cg_endo) cc_final: 0.7941 (Cg_exo) REVERT: O 98 TRP cc_start: 0.5955 (p-90) cc_final: 0.4515 (p-90) outliers start: 21 outliers final: 15 residues processed: 94 average time/residue: 0.1195 time to fit residues: 17.4887 Evaluate side-chains 88 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1054 MET Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 121 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 52 optimal weight: 0.1980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 96 GLN O 151 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.107199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.082846 restraints weight = 80733.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.083397 restraints weight = 44785.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.083632 restraints weight = 35542.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.083950 restraints weight = 27985.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.084031 restraints weight = 24075.393| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.5678 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= 0.110 Angle : 0.516 10.209 23346 Z= 0.284 Chirality : 0.036 0.214 2850 Planarity : 0.004 0.048 2013 Dihedral : 23.905 174.245 5520 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.02 % Favored : 96.90 % Rotamer: Outliers : 1.96 % Allowed : 13.50 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.24), residues: 1227 helix: 1.05 (0.21), residues: 579 sheet: -0.55 (0.48), residues: 127 loop : -0.78 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 485 TYR 0.017 0.001 TYR A 168 PHE 0.013 0.001 PHE A 27 TRP 0.008 0.001 TRP A 371 HIS 0.003 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (16323) covalent geometry : angle 0.51613 / 0.28 (23346) hydrogen bonds : bond 0.04821 / 3.20 ( 632) hydrogen bonds : angle 4.05536 / 2.97 ( 1672) *********************** 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 97 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 873 VAL cc_start: 0.7349 (OUTLIER) cc_final: 0.6998 (t) REVERT: A 1038 ASP cc_start: 0.8082 (m-30) cc_final: 0.7678 (m-30) REVERT: M 62 ILE cc_start: 0.7698 (mm) cc_final: 0.6923 (mm) REVERT: M 63 MET cc_start: 0.9368 (OUTLIER) cc_final: 0.8845 (mpp) REVERT: M 66 PHE cc_start: 0.8728 (m-10) cc_final: 0.8158 (m-80) REVERT: M 73 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.7733 (mmm160) REVERT: O 97 PRO cc_start: 0.8245 (Cg_endo) cc_final: 0.8029 (Cg_exo) REVERT: O 98 TRP cc_start: 0.6029 (p-90) cc_final: 0.4571 (p-90) REVERT: O 215 GLU cc_start: 0.6882 (pm20) cc_final: 0.6636 (pm20) outliers start: 21 outliers final: 15 residues processed: 93 average time/residue: 0.1201 time to fit residues: 17.0021 Evaluate side-chains 91 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1015 CYS Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1054 MET Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 MET 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: 1.9990 chunk 113 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS A 969 ASN O 151 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.105027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.078445 restraints weight = 79436.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.079975 restraints weight = 42045.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.080990 restraints weight = 30126.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.081204 restraints weight = 25357.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.081204 restraints weight = 23746.888| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.6040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16323 Z= 0.168 Angle : 0.566 10.414 23346 Z= 0.310 Chirality : 0.038 0.225 2850 Planarity : 0.004 0.045 2013 Dihedral : 23.948 175.839 5520 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.67 % Favored : 96.17 % Rotamer: Outliers : 2.05 % Allowed : 13.69 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1227 helix: 0.98 (0.21), residues: 580 sheet: -0.37 (0.50), residues: 115 loop : -0.74 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 32 TYR 0.014 0.002 TYR A 949 PHE 0.019 0.002 PHE A 870 TRP 0.011 0.002 TRP A 371 HIS 0.007 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (16323) covalent geometry : angle 0.56554 / 0.31 (23346) hydrogen bonds : bond 0.05765 / 3.92 ( 632) hydrogen bonds : angle 4.19189 / 3.07 ( 1672) *********************** 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 99 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 849 MET cc_start: 0.7557 (ttp) cc_final: 0.7286 (tmm) REVERT: A 873 VAL cc_start: 0.7623 (OUTLIER) cc_final: 0.7300 (t) REVERT: A 969 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.7977 (t0) REVERT: A 1038 ASP cc_start: 0.8116 (m-30) cc_final: 0.7697 (m-30) REVERT: M 62 ILE cc_start: 0.7556 (mm) cc_final: 0.6953 (mm) REVERT: M 63 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.8911 (mpp) REVERT: M 66 PHE cc_start: 0.8714 (m-10) cc_final: 0.8145 (m-80) REVERT: M 73 ARG cc_start: 0.8381 (mmm-85) cc_final: 0.7811 (mmm160) REVERT: O 97 PRO cc_start: 0.8271 (Cg_endo) cc_final: 0.8007 (Cg_exo) REVERT: O 98 TRP cc_start: 0.5929 (p-90) cc_final: 0.4591 (p-90) outliers start: 22 outliers final: 15 residues processed: 93 average time/residue: 0.1171 time to fit residues: 16.5526 Evaluate side-chains 92 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1015 CYS Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1054 MET Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 126 optimal weight: 6.9990 chunk 65 optimal weight: 0.0980 chunk 38 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 81 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.105478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.081237 restraints weight = 79985.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.081161 restraints weight = 48224.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.082174 restraints weight = 34800.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.082230 restraints weight = 25831.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.082324 restraints weight = 24971.400| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.6169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16323 Z= 0.134 Angle : 0.542 10.762 23346 Z= 0.297 Chirality : 0.036 0.231 2850 Planarity : 0.004 0.045 2013 Dihedral : 23.921 175.448 5520 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.50 % Favored : 96.33 % Rotamer: Outliers : 1.49 % Allowed : 14.15 % Favored : 84.36 % 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: 0.22 (0.24), residues: 1227 helix: 1.06 (0.21), residues: 578 sheet: -0.26 (0.52), residues: 113 loop : -0.73 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 968 TYR 0.015 0.001 TYR A 168 PHE 0.013 0.002 PHE A 975 TRP 0.009 0.001 TRP A 371 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (16323) covalent geometry : angle 0.54197 / 0.30 (23346) hydrogen bonds : bond 0.05254 / 3.54 ( 632) hydrogen bonds : angle 4.13943 / 3.03 ( 1672) ********************** 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 90 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 873 VAL cc_start: 0.7589 (OUTLIER) cc_final: 0.7238 (t) REVERT: A 1038 ASP cc_start: 0.8089 (m-30) cc_final: 0.7664 (m-30) REVERT: M 62 ILE cc_start: 0.7791 (mm) cc_final: 0.6928 (mm) REVERT: M 63 MET cc_start: 0.9334 (OUTLIER) cc_final: 0.8764 (mpp) REVERT: M 66 PHE cc_start: 0.8788 (m-10) cc_final: 0.8093 (m-80) REVERT: M 73 ARG cc_start: 0.8504 (mmm-85) cc_final: 0.7811 (mmm160) REVERT: O 97 PRO cc_start: 0.8245 (Cg_endo) cc_final: 0.8037 (Cg_exo) REVERT: O 98 TRP cc_start: 0.6175 (p-90) cc_final: 0.4701 (p-90) outliers start: 16 outliers final: 13 residues processed: 87 average time/residue: 0.1086 time to fit residues: 14.8935 Evaluate side-chains 88 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1015 CYS Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 144 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 87 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 72 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 969 ASN ** A1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.104878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.078120 restraints weight = 79141.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.079837 restraints weight = 42304.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.080862 restraints weight = 30124.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.081329 restraints weight = 25249.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.081636 restraints weight = 23288.141| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16323 Z= 0.142 Angle : 0.544 10.500 23346 Z= 0.298 Chirality : 0.036 0.248 2850 Planarity : 0.004 0.044 2013 Dihedral : 23.909 175.556 5520 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.50 % Favored : 96.33 % Rotamer: Outliers : 2.05 % Allowed : 13.69 % Favored : 84.26 % 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: 0.28 (0.24), residues: 1227 helix: 1.04 (0.22), residues: 573 sheet: -0.13 (0.53), residues: 113 loop : -0.61 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 32 TYR 0.012 0.001 TYR A 168 PHE 0.013 0.002 PHE A 975 TRP 0.012 0.001 TRP A 371 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (16323) covalent geometry : angle 0.54449 / 0.30 (23346) hydrogen bonds : bond 0.05361 / 3.58 ( 632) hydrogen bonds : angle 4.14497 / 3.03 ( 1672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2692.76 seconds wall clock time: 47 minutes 19.56 seconds (2839.56 seconds total)