Starting phenix.real_space_refine on Sat Oct 24 18:07:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bg9_12174/10_2026/7bg9_12174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bg9_12174/10_2026/7bg9_12174.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 { model { file = "/net/cci-nas-00/data/ceres_data/7bg9_12174/10_2026/7bg9_12174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bg9_12174/10_2026/7bg9_12174_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bg9_12174/10_2026/7bg9_12174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bg9_12174/10_2026/7bg9_12174.map" } 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 262 5.49 5 S 37 5.16 5 C 8028 2.51 5 N 2586 2.21 5 O 3320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14233 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 913, 7333 Classifications: {'peptide': 913} Link IDs: {'PTRANS': 51, 'TRANS': 861} Chain breaks: 4 Chain: "N" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} 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: "L" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 643 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "B" Number of atoms: 5431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 5431 Classifications: {'RNA': 256} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 10, 'rna3p_pur': 103, 'rna3p_pyr': 130} Link IDs: {'rna2p': 23, 'rna3p': 232} Chain breaks: 3 Time building chain proxies: 2.96, per 1000 atoms: 0.21 Number of scatterers: 14233 At special positions: 0 Unit cell: (134.31, 139.86, 135.42, 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 37 16.00 P 262 15.00 O 3320 8.00 N 2586 7.00 C 8028 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 463.3 milliseconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 54.7% alpha, 6.5% beta 70 base pairs and 128 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.727A pdb=" N ARG A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER A 16 " --> pdb=" O SER A 12 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 21 " --> pdb=" O HIS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 78 through 88 removed outlier: 4.297A pdb=" N VAL A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG A 87 " --> pdb=" O ARG A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 removed outlier: 4.322A pdb=" N PHE A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 100' Processing helix chain 'A' and resid 133 through 145 removed outlier: 3.543A pdb=" N LEU A 141 " --> pdb=" O TRP A 137 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 4.113A pdb=" N ALA A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.630A pdb=" N LYS A 329 " --> pdb=" O TYR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 349 removed outlier: 3.523A pdb=" N LEU A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 366 removed outlier: 4.184A pdb=" N ARG A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 Processing helix chain 'A' and resid 389 through 402 removed outlier: 4.044A pdb=" N PHE A 393 " --> pdb=" O MET A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.593A pdb=" N VAL A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 470 removed outlier: 4.117A pdb=" N GLY A 463 " --> pdb=" O TRP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 4.012A pdb=" N TRP A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 474 through 479' Processing helix chain 'A' and resid 480 through 496 removed outlier: 4.259A pdb=" N GLU A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 558 removed outlier: 3.599A pdb=" N ILE A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 595 removed outlier: 3.574A pdb=" N LYS A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 595 " --> pdb=" O GLN A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 610 removed outlier: 3.839A pdb=" N GLN A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 672 removed outlier: 3.509A pdb=" N VAL A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 670 " --> pdb=" O ASN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 676 Processing helix chain 'A' and resid 683 through 697 removed outlier: 3.587A pdb=" N THR A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 733 removed outlier: 4.204A pdb=" N LEU A 725 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 731 " --> pdb=" O GLU A 727 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE A 732 " --> pdb=" O VAL A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 781 Processing helix chain 'A' and resid 782 through 784 No H-bonds generated for 'chain 'A' and resid 782 through 784' Processing helix chain 'A' and resid 801 through 815 removed outlier: 3.706A pdb=" N PHE A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 854 removed outlier: 3.541A pdb=" N CYS A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 846 " --> pdb=" O CYS A 842 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN A 851 " --> pdb=" O GLY A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 889 removed outlier: 3.843A pdb=" N ALA A 880 " --> pdb=" O HIS A 876 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 removed outlier: 3.854A pdb=" N SER A 957 " --> pdb=" O SER A 953 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 958 " --> pdb=" O ILE A 954 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 953 through 958' Processing helix chain 'A' and resid 965 through 982 removed outlier: 3.810A pdb=" N ARG A 972 " --> pdb=" O ARG A 968 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 980 " --> pdb=" O GLY A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 removed outlier: 3.725A pdb=" N LEU A 987 " --> pdb=" O HIS A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1017 removed outlier: 4.017A pdb=" N THR A 999 " --> pdb=" O GLN A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1027 removed outlier: 3.531A pdb=" N LYS A1027 " --> pdb=" O GLN A1024 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1024 through 1027' Processing helix chain 'A' and resid 1028 through 1052 removed outlier: 4.230A pdb=" N PHE A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A1033 " --> pdb=" O PRO A1029 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP A1038 " --> pdb=" O ARG A1034 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A1042 " --> pdb=" O ASP A1038 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN A1051 " --> pdb=" O LEU A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1083 removed outlier: 4.412A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS A1075 " --> pdb=" O GLN A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1090 removed outlier: 3.903A pdb=" N TYR A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1106 removed outlier: 3.901A pdb=" N ALA A1099 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1119 removed outlier: 3.510A pdb=" N THR A1113 " --> pdb=" O GLY A1109 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A1118 " --> pdb=" O ALA A1114 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 50 removed outlier: 3.801A pdb=" N TYR M 43 " --> pdb=" O SER M 39 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN M 48 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL M 49 " --> pdb=" O VAL M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 86 removed outlier: 4.108A pdb=" N SER M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE M 66 " --> pdb=" O ILE M 62 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL M 67 " --> pdb=" O MET M 63 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN M 68 " --> pdb=" O ASN M 64 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE M 70 " --> pdb=" O PHE M 66 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE M 74 " --> pdb=" O ILE M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 103 removed outlier: 4.193A pdb=" N ILE M 95 " --> pdb=" O THR M 91 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN M 96 " --> pdb=" O SER M 92 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR M 97 " --> pdb=" O ARG M 93 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL M 99 " --> pdb=" O ILE M 95 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG M 100 " --> pdb=" O GLN M 96 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU M 101 " --> pdb=" O THR M 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 124 removed outlier: 3.550A pdb=" N LYS M 109 " --> pdb=" O GLY M 105 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS M 121 " --> pdb=" O LYS M 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 23 Processing helix chain 'L' and resid 27 through 35 removed outlier: 3.517A pdb=" N LEU L 35 " --> pdb=" O VAL L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 74 removed outlier: 4.561A pdb=" N VAL L 50 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR L 51 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL L 55 " --> pdb=" O TYR L 51 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU L 56 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU L 57 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR L 58 " --> pdb=" O ALA L 54 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU L 64 " --> pdb=" O THR L 60 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU L 66 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA L 67 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP L 73 " --> pdb=" O ASN L 69 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN L 74 " --> pdb=" O ALA L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 91 removed outlier: 3.810A pdb=" N ALA L 87 " --> pdb=" O HIS L 83 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG L 89 " --> pdb=" O GLN L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 98 removed outlier: 3.596A pdb=" N LEU L 97 " --> pdb=" O GLU L 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 4.151A pdb=" N LEU A 24 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 58 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 561 through 564 Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 600 Processing sheet with id=AA4, first strand: chain 'A' and resid 619 through 625 Processing sheet with id=AA5, first strand: chain 'A' and resid 862 through 866 removed outlier: 3.722A pdb=" N LEU A 866 " --> pdb=" O ASP A 869 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 711 " --> pdb=" O PHE A 870 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 905 " --> pdb=" O LYS A 710 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 755 through 761 removed outlier: 3.598A pdb=" N TYR A 744 " --> pdb=" O LYS A 757 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 928 through 930 Processing sheet with id=AA8, first strand: chain 'M' and resid 89 through 90 removed outlier: 3.757A pdb=" N ILE M 90 " --> pdb=" O ARG L 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 339 hydrogen bonds defined for protein. 972 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 182 hydrogen bonds 350 hydrogen bond angles 0 basepair planarities 70 basepair parallelities 128 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1592 1.29 - 1.43: 5038 1.43 - 1.56: 7769 1.56 - 1.70: 613 1.70 - 1.84: 51 Bond restraints: 15063 Sorted by residual: bond pdb=" CA VAL A 529 " pdb=" C VAL A 529 " ideal model delta sigma weight residual 1.524 1.622 -0.097 1.05e-02 9.07e+03 8.57e+01 bond pdb=" C VAL A 529 " pdb=" N PRO A 530 " ideal model delta sigma weight residual 1.328 1.441 -0.113 1.25e-02 6.40e+03 8.22e+01 bond pdb=" C PHE A 560 " pdb=" O PHE A 560 " ideal model delta sigma weight residual 1.235 1.148 0.088 1.02e-02 9.61e+03 7.37e+01 bond pdb=" O3' U B 177 " pdb=" P G B 178 " ideal model delta sigma weight residual 1.607 1.707 -0.100 1.20e-02 6.94e+03 6.95e+01 bond pdb=" C GLN A1023 " pdb=" O GLN A1023 " ideal model delta sigma weight residual 1.235 1.327 -0.092 1.14e-02 7.69e+03 6.49e+01 ... (remaining 15058 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 20524 3.29 - 6.59: 998 6.59 - 9.88: 93 9.88 - 13.18: 22 13.18 - 16.47: 5 Bond angle restraints: 21642 Sorted by residual: angle pdb=" N LYS A 410 " pdb=" CA LYS A 410 " pdb=" C LYS A 410 " ideal model delta sigma weight residual 112.68 99.30 13.38 1.33e+00 5.65e-01 1.01e+02 angle pdb=" N ASP A 337 " pdb=" CA ASP A 337 " pdb=" C ASP A 337 " ideal model delta sigma weight residual 111.02 123.23 -12.21 1.22e+00 6.72e-01 1.00e+02 angle pdb=" N PHE A 561 " pdb=" CA PHE A 561 " pdb=" C PHE A 561 " ideal model delta sigma weight residual 108.76 125.23 -16.47 1.69e+00 3.50e-01 9.50e+01 angle pdb=" C VAL A 529 " pdb=" N PRO A 530 " pdb=" CA PRO A 530 " ideal model delta sigma weight residual 120.85 110.36 10.49 1.08e+00 8.57e-01 9.44e+01 angle pdb=" N LYS A 338 " pdb=" CA LYS A 338 " pdb=" C LYS A 338 " ideal model delta sigma weight residual 111.71 122.61 -10.90 1.15e+00 7.56e-01 8.99e+01 ... (remaining 21637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 8712 35.65 - 71.29: 690 71.29 - 106.94: 111 106.94 - 142.59: 6 142.59 - 178.24: 7 Dihedral angle restraints: 9526 sinusoidal: 6373 harmonic: 3153 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 73.18 73.82 1 8.00e+00 1.56e-02 1.08e+02 dihedral pdb=" O4' U B 316 " pdb=" C1' U B 316 " pdb=" N1 U B 316 " pdb=" C2 U B 316 " ideal model delta sinusoidal sigma weight residual -160.00 16.07 -176.07 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" C4' U B 307 " pdb=" C3' U B 307 " pdb=" C2' U B 307 " pdb=" C1' U B 307 " ideal model delta sinusoidal sigma weight residual -35.00 23.52 -58.52 1 8.00e+00 1.56e-02 7.17e+01 ... (remaining 9523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 2422 0.156 - 0.313: 209 0.313 - 0.469: 22 0.469 - 0.625: 2 0.625 - 0.782: 3 Chirality restraints: 2658 Sorted by residual: chirality pdb=" C3' U B 312 " pdb=" C4' U B 312 " pdb=" O3' U B 312 " pdb=" C2' U B 312 " both_signs ideal model delta sigma weight residual False -2.48 -1.70 -0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" C3' G B 300 " pdb=" C4' G B 300 " pdb=" O3' G B 300 " pdb=" C2' G B 300 " both_signs ideal model delta sigma weight residual False -2.74 -2.07 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C3' A B 176 " pdb=" C4' A B 176 " pdb=" O3' A B 176 " pdb=" C2' A B 176 " both_signs ideal model delta sigma weight residual False -2.74 -2.11 -0.63 2.00e-01 2.50e+01 9.94e+00 ... (remaining 2655 not shown) Planarity restraints: 1784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA N 15 " 0.077 2.00e-02 2.50e+03 3.25e-02 2.90e+01 pdb=" N9 DA N 15 " -0.034 2.00e-02 2.50e+03 pdb=" C8 DA N 15 " -0.015 2.00e-02 2.50e+03 pdb=" N7 DA N 15 " -0.018 2.00e-02 2.50e+03 pdb=" C5 DA N 15 " -0.018 2.00e-02 2.50e+03 pdb=" C6 DA N 15 " 0.028 2.00e-02 2.50e+03 pdb=" N6 DA N 15 " 0.039 2.00e-02 2.50e+03 pdb=" N1 DA N 15 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DA N 15 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DA N 15 " -0.017 2.00e-02 2.50e+03 pdb=" C4 DA N 15 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 177 " -0.073 2.00e-02 2.50e+03 3.57e-02 2.86e+01 pdb=" N1 U B 177 " 0.034 2.00e-02 2.50e+03 pdb=" C2 U B 177 " 0.023 2.00e-02 2.50e+03 pdb=" O2 U B 177 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U B 177 " 0.021 2.00e-02 2.50e+03 pdb=" C4 U B 177 " -0.007 2.00e-02 2.50e+03 pdb=" O4 U B 177 " -0.051 2.00e-02 2.50e+03 pdb=" C5 U B 177 " 0.018 2.00e-02 2.50e+03 pdb=" C6 U B 177 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 547 " 0.043 2.00e-02 2.50e+03 3.25e-02 2.64e+01 pdb=" CG TRP A 547 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 547 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A 547 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 547 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP A 547 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP A 547 " -0.067 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 547 " 0.039 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 547 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 547 " 0.016 2.00e-02 2.50e+03 ... (remaining 1781 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 18 2.38 - 3.01: 6647 3.01 - 3.64: 21617 3.64 - 4.27: 32552 4.27 - 4.90: 47474 Nonbonded interactions: 108308 Sorted by model distance: nonbonded pdb=" CB PRO A 23 " pdb=" CZ3 TRP A 60 " model vdw 1.745 3.740 nonbonded pdb=" ND1 HIS A1022 " pdb=" O2' U B 312 " model vdw 1.946 3.120 nonbonded pdb=" CG PRO A 23 " pdb=" CZ3 TRP A 60 " model vdw 2.132 3.740 nonbonded pdb=" CE2 TRP A 510 " pdb=" NE2 HIS A1022 " model vdw 2.209 2.672 nonbonded pdb=" C VAL A 529 " pdb=" N6 A B 318 " model vdw 2.238 3.350 ... (remaining 108303 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.470 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.013 0.143 15064 Z= 0.924 Angle : 1.603 16.474 21642 Z= 1.049 Chirality : 0.098 0.782 2658 Planarity : 0.009 0.101 1784 Dihedral : 22.530 178.236 7486 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 1.59 % Allowed : 11.95 % Favored : 86.46 % Rotamer: Outliers : 0.75 % Allowed : 10.39 % Favored : 88.87 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -5.05 (0.20), residues: 1071 helix: -3.42 (0.15), residues: 461 sheet: -3.45 (0.47), residues: 66 loop : -3.29 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG A1011 TYR 0.050 0.008 TYR A 325 PHE 0.067 0.009 PHE A 575 TRP 0.067 0.009 TRP A 547 HIS 0.023 0.004 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.01342 / 0.92 (15063) covalent geometry : angle 1.60259 / 1.05 (21642) hydrogen bonds : bond 0.29173 / 19.27 ( 521) hydrogen bonds : angle 9.52310 / 6.69 ( 1322) Misc. bond : bond 0.08793 / 4.63 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 184 time to evaluate : 0.367 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8887 (tp30) cc_final: 0.8649 (tm-30) REVERT: A 60 TRP cc_start: 0.5856 (p90) cc_final: 0.5106 (p-90) REVERT: A 91 ARG cc_start: 0.4298 (tpt170) cc_final: 0.3907 (mmm-85) REVERT: A 152 LEU cc_start: 0.8796 (mp) cc_final: 0.8445 (tt) REVERT: A 345 PHE cc_start: 0.8013 (t80) cc_final: 0.7797 (t80) REVERT: A 347 LEU cc_start: 0.9199 (mp) cc_final: 0.8922 (tt) REVERT: A 450 GLN cc_start: 0.8956 (mm110) cc_final: 0.8437 (tp40) REVERT: A 491 THR cc_start: 0.8828 (m) cc_final: 0.8528 (m) REVERT: A 502 LYS cc_start: 0.8544 (mttp) cc_final: 0.8329 (ptmm) REVERT: A 511 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8545 (ttmt) REVERT: A 553 VAL cc_start: 0.8552 (t) cc_final: 0.8334 (p) REVERT: A 559 SER cc_start: 0.8315 (t) cc_final: 0.7863 (t) REVERT: A 560 PHE cc_start: 0.8958 (m-80) cc_final: 0.8711 (m-10) REVERT: A 607 ARG cc_start: 0.8953 (mmt-90) cc_final: 0.8602 (mpt180) REVERT: A 608 GLN cc_start: 0.9012 (mp10) cc_final: 0.8445 (pp30) REVERT: A 610 ARG cc_start: 0.8892 (mtt180) cc_final: 0.8629 (mtt180) REVERT: A 766 LEU cc_start: 0.8398 (mm) cc_final: 0.7832 (tt) REVERT: A 770 GLN cc_start: 0.9170 (mt0) cc_final: 0.8476 (mm110) REVERT: A 813 MET cc_start: 0.9261 (ptm) cc_final: 0.9031 (ppp) REVERT: A 854 PHE cc_start: 0.7242 (m-80) cc_final: 0.6997 (m-10) REVERT: A 893 GLU cc_start: 0.9557 (mt-10) cc_final: 0.9328 (tm-30) REVERT: A 899 ASN cc_start: 0.9187 (m-40) cc_final: 0.8828 (p0) REVERT: A 922 MET cc_start: 0.7376 (ptp) cc_final: 0.6949 (mpp) REVERT: A 941 GLU cc_start: 0.8450 (tt0) cc_final: 0.7884 (tm-30) REVERT: M 41 TYR cc_start: 0.9139 (m-80) cc_final: 0.8847 (m-10) REVERT: M 55 ILE cc_start: 0.8213 (tp) cc_final: 0.7880 (tt) REVERT: M 63 MET cc_start: 0.9586 (ptt) cc_final: 0.9067 (mmt) REVERT: M 73 ARG cc_start: 0.9100 (mmt-90) cc_final: 0.8690 (mtp180) REVERT: M 122 TYR cc_start: 0.8569 (t80) cc_final: 0.7785 (t80) REVERT: L 18 ARG cc_start: 0.7398 (mtm110) cc_final: 0.6946 (mtm-85) REVERT: L 40 TYR cc_start: 0.7600 (m-80) cc_final: 0.7323 (m-80) REVERT: L 62 GLU cc_start: 0.8939 (tp30) cc_final: 0.8653 (tt0) REVERT: L 69 ASN cc_start: 0.8027 (m-40) cc_final: 0.7779 (m110) REVERT: L 72 ARG cc_start: 0.8190 (ttp-110) cc_final: 0.7946 (mtp-110) REVERT: L 75 LYS cc_start: 0.7682 (tppt) cc_final: 0.7368 (ttpp) REVERT: L 91 ASP cc_start: 0.8345 (t70) cc_final: 0.7936 (t70) outliers start: 7 outliers final: 1 residues processed: 190 average time/residue: 0.1548 time to fit residues: 39.3413 Evaluate side-chains 126 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 511 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS A 40 GLN A 169 GLN ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN A 546 HIS A 571 ASN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 GLN A 995 GLN ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.111431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.073789 restraints weight = 48439.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.075598 restraints weight = 27396.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.076659 restraints weight = 19874.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.077296 restraints weight = 16819.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.077540 restraints weight = 15399.835| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15064 Z= 0.211 Angle : 0.844 10.039 21642 Z= 0.455 Chirality : 0.051 0.661 2658 Planarity : 0.007 0.077 1784 Dihedral : 23.599 179.679 5384 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.72 % Favored : 93.09 % Rotamer: Outliers : 2.46 % Allowed : 14.67 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.56 (0.23), residues: 1071 helix: -1.81 (0.20), residues: 514 sheet: -2.67 (0.48), residues: 72 loop : -2.90 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 30 TYR 0.020 0.003 TYR A 552 PHE 0.025 0.003 PHE A 708 TRP 0.029 0.003 TRP A 60 HIS 0.027 0.002 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.21 (15063) covalent geometry : angle 0.84421 / 0.45 (21642) hydrogen bonds : bond 0.09145 / 6.06 ( 521) hydrogen bonds : angle 5.36491 / 3.86 ( 1322) Misc. bond : bond 0.00147 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.395 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: symmetry clash REVERT: A 152 LEU cc_start: 0.8797 (mp) cc_final: 0.8425 (tt) REVERT: A 347 LEU cc_start: 0.8897 (mp) cc_final: 0.8447 (tt) REVERT: A 762 HIS cc_start: 0.7179 (t-90) cc_final: 0.6863 (t-90) REVERT: A 770 GLN cc_start: 0.8899 (mt0) cc_final: 0.8110 (mm110) REVERT: A 772 TYR cc_start: 0.6937 (OUTLIER) cc_final: 0.6320 (m-80) REVERT: M 63 MET cc_start: 0.9232 (ptt) cc_final: 0.8849 (mmt) REVERT: M 69 ASP cc_start: 0.8365 (t0) cc_final: 0.8128 (t0) REVERT: M 73 ARG cc_start: 0.9144 (mmt-90) cc_final: 0.8928 (mtm-85) REVERT: M 122 TYR cc_start: 0.8312 (t80) cc_final: 0.7901 (t80) REVERT: L 18 ARG cc_start: 0.7264 (mtm110) cc_final: 0.6951 (mtm-85) REVERT: L 75 LYS cc_start: 0.7735 (tppt) cc_final: 0.7481 (tttp) REVERT: L 96 LYS cc_start: 0.8728 (tppt) cc_final: 0.8375 (mppt) outliers start: 23 outliers final: 11 residues processed: 138 average time/residue: 0.1420 time to fit residues: 27.0519 Evaluate side-chains 106 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [124, 111, 32, 115, 83, 68, 41, 59, 45, 19, 97] chunk 124 optimal weight: 50.0000 chunk 111 optimal weight: 50.0000 chunk 32 optimal weight: 0.0050 chunk 115 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.0010 chunk 19 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.113348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.076266 restraints weight = 48995.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.078184 restraints weight = 26993.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.079317 restraints weight = 19276.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.079998 restraints weight = 16263.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.080275 restraints weight = 14784.254| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15064 Z= 0.146 Angle : 0.673 8.966 21642 Z= 0.366 Chirality : 0.041 0.505 2658 Planarity : 0.006 0.069 1784 Dihedral : 23.339 178.825 5380 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.21 % Allowed : 15.74 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.59 (0.24), residues: 1071 helix: -0.84 (0.21), residues: 523 sheet: -2.26 (0.51), residues: 79 loop : -2.63 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 577 TYR 0.027 0.002 TYR A 18 PHE 0.022 0.002 PHE A 159 TRP 0.034 0.002 TRP A 60 HIS 0.005 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (15063) covalent geometry : angle 0.67293 / 0.37 (21642) hydrogen bonds : bond 0.06611 / 4.37 ( 521) hydrogen bonds : angle 4.55185 / 3.29 ( 1322) Misc. bond : bond 0.00098 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LEU cc_start: 0.8771 (mp) cc_final: 0.8400 (tp) REVERT: A 347 LEU cc_start: 0.8882 (mp) cc_final: 0.8499 (tt) REVERT: A 685 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7791 (m-30) REVERT: A 770 GLN cc_start: 0.8860 (mt0) cc_final: 0.8134 (mm110) REVERT: A 772 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.6280 (m-80) REVERT: A 829 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7367 (tm-30) REVERT: M 63 MET cc_start: 0.9219 (ptt) cc_final: 0.8839 (mmt) REVERT: M 72 GLU cc_start: 0.9240 (mm-30) cc_final: 0.9025 (mm-30) REVERT: M 73 ARG cc_start: 0.9167 (mmt-90) cc_final: 0.8958 (mtm-85) REVERT: M 122 TYR cc_start: 0.8360 (t80) cc_final: 0.7707 (t80) REVERT: L 18 ARG cc_start: 0.7246 (mtm110) cc_final: 0.6959 (mtm-85) REVERT: L 75 LYS cc_start: 0.7811 (tppt) cc_final: 0.7563 (tttp) outliers start: 30 outliers final: 12 residues processed: 132 average time/residue: 0.1146 time to fit residues: 21.9869 Evaluate side-chains 109 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 896 CYS Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1090 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [3, 46, 97, 93, 2, 101, 7, 22, 94, 42, 41] chunk 3 optimal weight: 20.0000 chunk 46 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.112182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.076172 restraints weight = 49640.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.077892 restraints weight = 29262.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.078362 restraints weight = 19404.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.078512 restraints weight = 21011.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.078512 restraints weight = 17776.925| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15064 Z= 0.151 Angle : 0.644 8.801 21642 Z= 0.347 Chirality : 0.041 0.521 2658 Planarity : 0.006 0.063 1784 Dihedral : 23.305 178.146 5378 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.10 % Allowed : 18.74 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.25), residues: 1071 helix: -0.30 (0.22), residues: 524 sheet: -1.98 (0.54), residues: 78 loop : -2.52 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 620 TYR 0.020 0.002 TYR A 168 PHE 0.019 0.002 PHE A 345 TRP 0.020 0.002 TRP A 60 HIS 0.006 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (15063) covalent geometry : angle 0.64447 / 0.35 (21642) hydrogen bonds : bond 0.06112 / 4.05 ( 521) hydrogen bonds : angle 4.32956 / 3.12 ( 1322) Misc. bond : bond 0.00082 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LEU cc_start: 0.8807 (mp) cc_final: 0.8566 (tt) REVERT: A 770 GLN cc_start: 0.8985 (mt0) cc_final: 0.8178 (mm110) REVERT: A 772 TYR cc_start: 0.7066 (t80) cc_final: 0.6298 (m-80) REVERT: A 894 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.6694 (t80) REVERT: M 63 MET cc_start: 0.9217 (ptt) cc_final: 0.8853 (mmt) REVERT: M 122 TYR cc_start: 0.8298 (t80) cc_final: 0.7717 (t80) REVERT: L 75 LYS cc_start: 0.7798 (tppt) cc_final: 0.7576 (tttp) REVERT: L 96 LYS cc_start: 0.8389 (tppt) cc_final: 0.8142 (tppt) outliers start: 29 outliers final: 18 residues processed: 120 average time/residue: 0.1281 time to fit residues: 22.1023 Evaluate side-chains 106 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 894 TYR Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain M residue 96 GLN Chi-restraints excluded: chain L residue 84 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [47, 72, 51, 114, 67, 2, 91, 95, 24, 9, 97] chunk 47 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 114 optimal weight: 40.0000 chunk 67 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 91 optimal weight: 0.3980 chunk 95 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 97 optimal weight: 0.0370 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS A 534 HIS A 608 GLN ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.113212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.076233 restraints weight = 50026.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.078142 restraints weight = 27225.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.079317 restraints weight = 19476.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.079909 restraints weight = 16290.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.080179 restraints weight = 14915.318| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 15064 Z= 0.124 Angle : 0.607 8.273 21642 Z= 0.329 Chirality : 0.039 0.466 2658 Planarity : 0.005 0.060 1784 Dihedral : 23.290 179.777 5378 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.75 % Allowed : 20.66 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.25), residues: 1071 helix: 0.02 (0.23), residues: 523 sheet: -1.75 (0.55), residues: 79 loop : -2.52 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 93 TYR 0.023 0.002 TYR A 18 PHE 0.023 0.002 PHE A 345 TRP 0.019 0.001 TRP A 60 HIS 0.008 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (15063) covalent geometry : angle 0.60729 / 0.33 (21642) hydrogen bonds : bond 0.05409 / 3.58 ( 521) hydrogen bonds : angle 4.09796 / 2.96 ( 1322) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 HIS cc_start: 0.6660 (OUTLIER) cc_final: 0.6429 (t70) REVERT: A 347 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8510 (tt) REVERT: A 608 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7155 (pp30) REVERT: A 762 HIS cc_start: 0.7438 (t-90) cc_final: 0.7161 (t-90) REVERT: A 770 GLN cc_start: 0.8815 (mt0) cc_final: 0.8053 (mm110) REVERT: A 772 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.6258 (m-80) REVERT: A 894 TYR cc_start: 0.7437 (OUTLIER) cc_final: 0.6581 (t80) REVERT: M 63 MET cc_start: 0.9287 (ptt) cc_final: 0.8872 (mmt) REVERT: M 69 ASP cc_start: 0.8274 (t0) cc_final: 0.7911 (t0) REVERT: M 73 ARG cc_start: 0.8034 (mtm-85) cc_final: 0.7739 (mtm180) REVERT: M 122 TYR cc_start: 0.8184 (t80) cc_final: 0.7872 (t80) REVERT: L 85 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8048 (pt0) REVERT: L 96 LYS cc_start: 0.8338 (tppt) cc_final: 0.8106 (tppt) outliers start: 35 outliers final: 15 residues processed: 118 average time/residue: 0.1126 time to fit residues: 19.8835 Evaluate side-chains 104 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 894 TYR Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain L residue 84 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [98, 79, 29, 41, 57, 116, 118, 9, 17, 54, 121] chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 118 optimal weight: 50.0000 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 121 optimal weight: 30.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS A 608 GLN A 925 HIS ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.112314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.075282 restraints weight = 49978.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.077080 restraints weight = 27526.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.078229 restraints weight = 19870.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.078679 restraints weight = 16693.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.078682 restraints weight = 15372.658| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15064 Z= 0.153 Angle : 0.632 9.135 21642 Z= 0.337 Chirality : 0.040 0.487 2658 Planarity : 0.005 0.060 1784 Dihedral : 23.288 179.378 5378 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.32 % Allowed : 21.31 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.25), residues: 1071 helix: 0.18 (0.23), residues: 521 sheet: -1.73 (0.56), residues: 78 loop : -2.49 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 607 TYR 0.020 0.002 TYR A 18 PHE 0.025 0.002 PHE A 345 TRP 0.019 0.001 TRP A 60 HIS 0.004 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (15063) covalent geometry : angle 0.63232 / 0.34 (21642) hydrogen bonds : bond 0.05710 / 3.79 ( 521) hydrogen bonds : angle 4.14908 / 2.98 ( 1322) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 HIS cc_start: 0.6683 (OUTLIER) cc_final: 0.6435 (t70) REVERT: A 347 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8525 (tt) REVERT: A 722 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7436 (mm110) REVERT: A 762 HIS cc_start: 0.7433 (t-90) cc_final: 0.7221 (t-90) REVERT: A 770 GLN cc_start: 0.8842 (mt0) cc_final: 0.8064 (mm110) REVERT: A 772 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.6194 (m-80) REVERT: A 894 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.6788 (t80) REVERT: M 63 MET cc_start: 0.9312 (ptt) cc_final: 0.8870 (mmt) REVERT: M 69 ASP cc_start: 0.8200 (t0) cc_final: 0.7790 (t0) REVERT: M 73 ARG cc_start: 0.8041 (mtm-85) cc_final: 0.7702 (mtm180) REVERT: M 122 TYR cc_start: 0.8100 (t80) cc_final: 0.7817 (t80) REVERT: L 85 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8027 (pt0) REVERT: L 96 LYS cc_start: 0.8338 (tppt) cc_final: 0.8102 (tppt) outliers start: 31 outliers final: 21 residues processed: 109 average time/residue: 0.1117 time to fit residues: 18.3383 Evaluate side-chains 111 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 722 GLN Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 894 TYR Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 84 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [15, 64, 128, 107, 48, 84, 109, 19, 75, 99, 41] chunk 15 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 128 optimal weight: 50.0000 chunk 107 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 50.0000 chunk 19 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS A 925 HIS ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.112432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.077448 restraints weight = 49369.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.077946 restraints weight = 29637.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.078704 restraints weight = 20849.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.078774 restraints weight = 19240.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.078765 restraints weight = 17460.020| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15064 Z= 0.141 Angle : 0.614 10.048 21642 Z= 0.329 Chirality : 0.039 0.471 2658 Planarity : 0.005 0.060 1784 Dihedral : 23.329 179.494 5378 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.64 % Allowed : 20.99 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.25), residues: 1071 helix: 0.25 (0.23), residues: 526 sheet: -1.69 (0.55), residues: 79 loop : -2.47 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 610 TYR 0.020 0.002 TYR A 18 PHE 0.016 0.002 PHE A 883 TRP 0.017 0.001 TRP A 60 HIS 0.004 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (15063) covalent geometry : angle 0.61423 / 0.33 (21642) hydrogen bonds : bond 0.05438 / 3.60 ( 521) hydrogen bonds : angle 4.09529 / 2.94 ( 1322) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8520 (tt) REVERT: A 722 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7478 (mm110) REVERT: A 762 HIS cc_start: 0.7565 (t-90) cc_final: 0.7286 (t-90) REVERT: A 770 GLN cc_start: 0.8868 (mt0) cc_final: 0.8051 (mm110) REVERT: A 772 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6301 (m-80) REVERT: A 773 MET cc_start: 0.5880 (ppp) cc_final: 0.5674 (tmm) REVERT: A 894 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.6866 (t80) REVERT: M 63 MET cc_start: 0.9303 (ptt) cc_final: 0.8908 (mmt) REVERT: M 122 TYR cc_start: 0.8047 (t80) cc_final: 0.7747 (t80) REVERT: L 85 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8069 (pt0) REVERT: L 96 LYS cc_start: 0.8351 (tppt) cc_final: 0.8104 (tppt) outliers start: 34 outliers final: 26 residues processed: 113 average time/residue: 0.1153 time to fit residues: 19.6326 Evaluate side-chains 113 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 18 TYR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 722 GLN Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 894 TYR Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 84 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [118, 22, 120, 76, 97, 6, 96, 75, 57, 60, 27] chunk 118 optimal weight: 50.0000 chunk 22 optimal weight: 0.2980 chunk 120 optimal weight: 50.0000 chunk 76 optimal weight: 0.9980 chunk 97 optimal weight: 0.0020 chunk 6 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 HIS ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.113759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.077959 restraints weight = 49356.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.079816 restraints weight = 29373.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.079826 restraints weight = 19695.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.080121 restraints weight = 18650.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.080170 restraints weight = 17180.931| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 15064 Z= 0.113 Angle : 0.587 9.286 21642 Z= 0.315 Chirality : 0.037 0.435 2658 Planarity : 0.005 0.060 1784 Dihedral : 23.313 178.964 5378 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.25 % Allowed : 22.81 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.26), residues: 1071 helix: 0.41 (0.23), residues: 525 sheet: -1.50 (0.58), residues: 79 loop : -2.36 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG M 93 TYR 0.021 0.001 TYR A 18 PHE 0.026 0.002 PHE A 345 TRP 0.014 0.001 TRP A 60 HIS 0.003 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (15063) covalent geometry : angle 0.58677 / 0.32 (21642) hydrogen bonds : bond 0.04713 / 3.11 ( 521) hydrogen bonds : angle 3.96442 / 2.88 ( 1322) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LEU cc_start: 0.8683 (mp) cc_final: 0.8439 (tt) REVERT: A 516 ASP cc_start: 0.6886 (m-30) cc_final: 0.6332 (p0) REVERT: A 631 ARG cc_start: 0.8409 (ttp-170) cc_final: 0.8136 (ptp-110) REVERT: A 722 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.6836 (mm110) REVERT: A 770 GLN cc_start: 0.8847 (mt0) cc_final: 0.8057 (mm110) REVERT: A 772 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6263 (m-80) REVERT: M 63 MET cc_start: 0.9176 (ptt) cc_final: 0.8914 (mmt) REVERT: M 122 TYR cc_start: 0.8035 (t80) cc_final: 0.7731 (t80) REVERT: L 85 GLN cc_start: 0.8712 (tm-30) cc_final: 0.7967 (pt0) REVERT: L 96 LYS cc_start: 0.8311 (tppt) cc_final: 0.8076 (tppt) outliers start: 21 outliers final: 18 residues processed: 105 average time/residue: 0.1182 time to fit residues: 18.4313 Evaluate side-chains 106 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 722 GLN Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 84 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [73, 40, 99, 90, 97, 113, 106, 80, 0, 117, 75] chunk 73 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 chunk 90 optimal weight: 0.0370 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 40.0000 chunk 106 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 30.0000 chunk 75 optimal weight: 0.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 GLN ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.113529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.077753 restraints weight = 49364.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.079483 restraints weight = 29571.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.079648 restraints weight = 19995.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.080293 restraints weight = 18222.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.080123 restraints weight = 16737.233| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15064 Z= 0.120 Angle : 0.599 10.688 21642 Z= 0.320 Chirality : 0.038 0.446 2658 Planarity : 0.005 0.058 1784 Dihedral : 23.309 179.538 5378 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.10 % Allowed : 22.38 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.26), residues: 1071 helix: 0.61 (0.23), residues: 520 sheet: -1.43 (0.60), residues: 79 loop : -2.30 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG M 93 TYR 0.019 0.001 TYR A 18 PHE 0.024 0.002 PHE A 345 TRP 0.014 0.001 TRP A 60 HIS 0.003 0.001 HIS A 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (15063) covalent geometry : angle 0.59868 / 0.32 (21642) hydrogen bonds : bond 0.04874 / 3.21 ( 521) hydrogen bonds : angle 3.98636 / 2.88 ( 1322) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 ASP cc_start: 0.6882 (m-30) cc_final: 0.6323 (p0) REVERT: A 631 ARG cc_start: 0.8440 (ttp-170) cc_final: 0.8152 (ptp-110) REVERT: A 770 GLN cc_start: 0.8820 (mt0) cc_final: 0.8051 (mm110) REVERT: A 772 TYR cc_start: 0.7195 (OUTLIER) cc_final: 0.6479 (m-80) REVERT: M 96 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7863 (mp10) REVERT: M 122 TYR cc_start: 0.8028 (t80) cc_final: 0.7725 (t80) REVERT: L 85 GLN cc_start: 0.8711 (tm-30) cc_final: 0.7960 (pt0) REVERT: L 96 LYS cc_start: 0.8304 (tppt) cc_final: 0.8065 (tppt) outliers start: 29 outliers final: 21 residues processed: 110 average time/residue: 0.1198 time to fit residues: 19.6595 Evaluate side-chains 110 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain M residue 96 GLN Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 84 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [126, 115, 24, 36, 14, 96, 92, 80, 43, 106, 61] chunk 126 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.114111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.080333 restraints weight = 49947.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.080483 restraints weight = 30612.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.080451 restraints weight = 22833.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.080860 restraints weight = 21443.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.080842 restraints weight = 18735.048| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15064 Z= 0.113 Angle : 0.595 10.445 21642 Z= 0.317 Chirality : 0.037 0.426 2658 Planarity : 0.005 0.074 1784 Dihedral : 23.314 179.130 5378 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.36 % Allowed : 22.59 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.26), residues: 1071 helix: 0.73 (0.23), residues: 520 sheet: -1.35 (0.60), residues: 80 loop : -2.26 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG M 93 TYR 0.019 0.001 TYR A 18 PHE 0.026 0.002 PHE A 345 TRP 0.013 0.001 TRP A 60 HIS 0.003 0.000 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (15063) covalent geometry : angle 0.59479 / 0.32 (21642) hydrogen bonds : bond 0.04525 / 2.98 ( 521) hydrogen bonds : angle 3.96759 / 2.88 ( 1322) Misc. bond : bond 0.00037 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 ASP cc_start: 0.6814 (m-30) cc_final: 0.6380 (p0) REVERT: A 631 ARG cc_start: 0.8424 (ttp-170) cc_final: 0.8160 (ptp-110) REVERT: A 770 GLN cc_start: 0.8810 (mt0) cc_final: 0.8076 (mm110) REVERT: A 772 TYR cc_start: 0.7098 (OUTLIER) cc_final: 0.6110 (m-80) REVERT: M 91 THR cc_start: 0.6968 (p) cc_final: 0.6505 (p) REVERT: M 96 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7917 (mp10) REVERT: M 122 TYR cc_start: 0.7975 (t80) cc_final: 0.7701 (t80) REVERT: L 85 GLN cc_start: 0.8700 (tm-30) cc_final: 0.7954 (pt0) REVERT: L 96 LYS cc_start: 0.8314 (tppt) cc_final: 0.8055 (tppt) outliers start: 22 outliers final: 18 residues processed: 105 average time/residue: 0.1178 time to fit residues: 18.4582 Evaluate side-chains 109 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain M residue 96 GLN Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [28, 32, 114, 10, 119, 93, 109, 58, 23, 52, 45] chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 114 optimal weight: 40.0000 chunk 10 optimal weight: 20.0000 chunk 119 optimal weight: 40.0000 chunk 93 optimal weight: 10.0000 chunk 109 optimal weight: 50.0000 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.111232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.076748 restraints weight = 50235.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.076620 restraints weight = 30307.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.077017 restraints weight = 21819.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.077219 restraints weight = 22216.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.077120 restraints weight = 19188.336| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 15064 Z= 0.218 Angle : 0.699 9.315 21642 Z= 0.369 Chirality : 0.044 0.509 2658 Planarity : 0.006 0.082 1784 Dihedral : 23.408 179.799 5378 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.78 % Allowed : 22.81 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.25), residues: 1071 helix: 0.44 (0.23), residues: 531 sheet: -1.47 (0.59), residues: 80 loop : -2.35 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 774 TYR 0.021 0.002 TYR A 18 PHE 0.024 0.002 PHE A 575 TRP 0.017 0.002 TRP A 60 HIS 0.008 0.001 HIS A 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (15063) covalent geometry : angle 0.69925 / 0.37 (21642) hydrogen bonds : bond 0.06275 / 4.12 ( 521) hydrogen bonds : angle 4.30980 / 3.12 ( 1322) Misc. bond : bond 0.00001 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2481.74 seconds wall clock time: 43 minutes 29.18 seconds (2609.18 seconds total)