Starting phenix.real_space_refine on Wed Mar 4 14:48:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bg9_12174/03_2026/7bg9_12174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bg9_12174/03_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_12174/03_2026/7bg9_12174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bg9_12174/03_2026/7bg9_12174_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bg9_12174/03_2026/7bg9_12174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bg9_12174/03_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-dev-5986/lib/python3.9/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: 3.05, 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: 1.28 Conformation dependent library (CDL) restraints added in 390.4 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: 1.88 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: 3.81 Time building geometry restraints manager: 1.68 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=" 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 bond pdb=" CA ILE A1004 " pdb=" C ILE A1004 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.22e-02 6.72e+03 4.84e+01 ... (remaining 15058 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 20386 3.29 - 6.59: 1132 6.59 - 9.88: 97 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: 2269 0.156 - 0.313: 356 0.313 - 0.469: 28 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: 1.460 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 15.650 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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= 0.879 Angle : 1.642 16.474 21642 Z= 1.041 Chirality : 0.110 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 covalent geometry : bond 0.01346 (15063) covalent geometry : angle 1.64204 (21642) hydrogen bonds : bond 0.29173 ( 521) hydrogen bonds : angle 9.52310 ( 1322) Misc. bond : bond 0.08793 ( 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 : 0.399 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: 0.3908 (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 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: 0.8698 (m-10) REVERT: M 44 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8191 (mttp) REVERT: M 55 ILE cc_start: 0.8213 (tp) cc_final: 0.7881 (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: 0.1661 time to fit residues: 41.6970 Evaluate side-chains 125 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: 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: 0.8980 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 40 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 A1100 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.112752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.075564 restraints weight = 48570.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.077448 restraints weight = 27100.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.078586 restraints weight = 19538.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.079202 restraints weight = 16384.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.079471 restraints weight = 14974.793| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15064 Z= 0.170 Angle : 0.744 9.115 21642 Z= 0.382 Chirality : 0.040 0.280 2658 Planarity : 0.006 0.070 1784 Dihedral : 23.460 179.734 5380 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.86 % Favored : 95.05 % Rotamer: Outliers : 3.00 % Allowed : 13.49 % Favored : 83.51 % 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: -3.12 (0.23), residues: 1071 helix: -1.36 (0.20), residues: 516 sheet: -2.63 (0.50), residues: 78 loop : -2.76 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 742 TYR 0.016 0.002 TYR A 18 PHE 0.024 0.002 PHE A 708 TRP 0.025 0.002 TRP A 60 HIS 0.015 0.002 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00352 (15063) covalent geometry : angle 0.74432 (21642) hydrogen bonds : bond 0.05997 ( 521) hydrogen bonds : angle 4.64994 ( 1322) Misc. bond : bond 0.00095 ( 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 164 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LEU cc_start: 0.8718 (mp) cc_final: 0.8318 (tt) REVERT: A 347 LEU cc_start: 0.8811 (mp) cc_final: 0.8501 (tt) REVERT: A 770 GLN cc_start: 0.8787 (mt0) cc_final: 0.8087 (mm110) REVERT: A 772 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.6319 (m-80) REVERT: M 44 LYS cc_start: 0.8372 (mtmt) cc_final: 0.8139 (mttp) REVERT: M 69 ASP cc_start: 0.8423 (t0) cc_final: 0.8159 (t0) REVERT: M 72 GLU cc_start: 0.9253 (mm-30) cc_final: 0.9009 (mm-30) REVERT: M 73 ARG cc_start: 0.9155 (mmt-90) cc_final: 0.8951 (mtm180) REVERT: M 122 TYR cc_start: 0.8260 (t80) cc_final: 0.7632 (t80) REVERT: L 18 ARG cc_start: 0.7244 (mtm110) cc_final: 0.6970 (mtm-85) REVERT: L 75 LYS cc_start: 0.7844 (tppt) cc_final: 0.7621 (tttp) outliers start: 28 outliers final: 10 residues processed: 152 average time/residue: 0.1357 time to fit residues: 28.6104 Evaluate side-chains 112 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 773 MET 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 M residue 57 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 40.0000 chunk 111 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.113192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.076393 restraints weight = 49262.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.078298 restraints weight = 26886.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.079417 restraints weight = 19022.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.080032 restraints weight = 15874.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.080395 restraints weight = 14484.722| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15064 Z= 0.137 Angle : 0.655 8.966 21642 Z= 0.335 Chirality : 0.037 0.256 2658 Planarity : 0.005 0.058 1784 Dihedral : 23.328 179.713 5380 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.46 % Allowed : 17.67 % Favored : 79.87 % 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: -1.91 (0.25), residues: 1071 helix: -0.15 (0.22), residues: 520 sheet: -2.51 (0.50), residues: 86 loop : -2.31 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 610 TYR 0.017 0.002 TYR M 41 PHE 0.016 0.002 PHE A 708 TRP 0.021 0.002 TRP A 60 HIS 0.012 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00289 (15063) covalent geometry : angle 0.65544 (21642) hydrogen bonds : bond 0.05009 ( 521) hydrogen bonds : angle 4.11004 ( 1322) Misc. bond : bond 0.00070 ( 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 132 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LEU cc_start: 0.8762 (mp) cc_final: 0.8498 (tt) REVERT: A 372 MET cc_start: 0.4856 (ppp) cc_final: 0.4009 (mmt) REVERT: A 770 GLN cc_start: 0.8784 (mt0) cc_final: 0.8089 (mm110) REVERT: A 772 TYR cc_start: 0.7172 (t80) cc_final: 0.6417 (m-80) REVERT: M 44 LYS cc_start: 0.8383 (mtmt) cc_final: 0.8064 (mttp) REVERT: M 122 TYR cc_start: 0.8202 (t80) cc_final: 0.7826 (t80) REVERT: L 18 ARG cc_start: 0.7218 (mtm110) cc_final: 0.6776 (mtm-85) REVERT: L 85 GLN cc_start: 0.8765 (tm-30) cc_final: 0.7997 (pt0) outliers start: 23 outliers final: 15 residues processed: 124 average time/residue: 0.1220 time to fit residues: 21.9791 Evaluate side-chains 108 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 618 THR 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 977 VAL 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 57 SER Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 3 optimal weight: 5.9990 chunk 46 optimal weight: 0.0980 chunk 97 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 42 optimal weight: 0.0000 chunk 41 optimal weight: 8.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 169 GLN A 608 GLN A 736 GLN A 737 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.115854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.081777 restraints weight = 51117.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.082681 restraints weight = 30652.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.083038 restraints weight = 21787.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.083265 restraints weight = 20173.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.083127 restraints weight = 18840.364| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15064 Z= 0.114 Angle : 0.599 8.790 21642 Z= 0.302 Chirality : 0.034 0.203 2658 Planarity : 0.005 0.053 1784 Dihedral : 23.240 178.971 5378 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.68 % Allowed : 20.02 % Favored : 77.30 % 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: -1.18 (0.26), residues: 1071 helix: 0.63 (0.23), residues: 509 sheet: -2.02 (0.54), residues: 87 loop : -2.17 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 80 TYR 0.016 0.001 TYR A 18 PHE 0.013 0.001 PHE A 393 TRP 0.020 0.001 TRP A 60 HIS 0.007 0.001 HIS A 762 Details of bonding type rmsd covalent geometry : bond 0.00229 (15063) covalent geometry : angle 0.59910 (21642) hydrogen bonds : bond 0.03944 ( 521) hydrogen bonds : angle 3.71420 ( 1322) Misc. bond : bond 0.00039 ( 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 134 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8416 (tt) REVERT: A 372 MET cc_start: 0.5330 (ppp) cc_final: 0.4627 (mmt) REVERT: A 631 ARG cc_start: 0.8486 (ttp-170) cc_final: 0.8242 (ptp-110) REVERT: A 770 GLN cc_start: 0.8739 (mt0) cc_final: 0.7994 (mm110) REVERT: A 772 TYR cc_start: 0.7204 (t80) cc_final: 0.6487 (m-80) REVERT: A 894 TYR cc_start: 0.7272 (OUTLIER) cc_final: 0.6362 (t80) REVERT: A 922 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7229 (ptt) REVERT: M 44 LYS cc_start: 0.8365 (mtmt) cc_final: 0.8115 (mttp) REVERT: M 122 TYR cc_start: 0.8143 (t80) cc_final: 0.7723 (t80) REVERT: L 18 ARG cc_start: 0.7006 (mtm110) cc_final: 0.6666 (mtm-85) REVERT: L 85 GLN cc_start: 0.8705 (tm-30) cc_final: 0.7918 (pt0) REVERT: L 86 LEU cc_start: 0.8648 (mt) cc_final: 0.8302 (mt) outliers start: 25 outliers final: 13 residues processed: 128 average time/residue: 0.1331 time to fit residues: 24.5332 Evaluate side-chains 111 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 894 TYR Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain M residue 81 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 47 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 97 optimal weight: 0.0050 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 534 HIS A 608 GLN A 737 ASN A 762 HIS ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.114715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.080870 restraints weight = 50336.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.081062 restraints weight = 31464.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.081145 restraints weight = 23141.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.081602 restraints weight = 22492.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.081566 restraints weight = 19410.363| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15064 Z= 0.125 Angle : 0.612 8.195 21642 Z= 0.309 Chirality : 0.035 0.203 2658 Planarity : 0.005 0.051 1784 Dihedral : 23.189 179.181 5378 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.18 % Allowed : 19.59 % Favored : 76.23 % 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: 0.72 (0.24), residues: 511 sheet: -1.50 (0.57), residues: 82 loop : -2.16 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 93 TYR 0.019 0.001 TYR A 18 PHE 0.021 0.001 PHE A 345 TRP 0.019 0.001 TRP A 60 HIS 0.007 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00263 (15063) covalent geometry : angle 0.61155 (21642) hydrogen bonds : bond 0.04843 ( 521) hydrogen bonds : angle 3.80818 ( 1322) Misc. bond : bond 0.00032 ( 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 138 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 MET cc_start: 0.5352 (ppp) cc_final: 0.4639 (mmm) REVERT: A 770 GLN cc_start: 0.8708 (mt0) cc_final: 0.7898 (mm110) REVERT: A 772 TYR cc_start: 0.7364 (t80) cc_final: 0.6280 (m-80) REVERT: A 774 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.6846 (ptt-90) REVERT: M 44 LYS cc_start: 0.8430 (mtmt) cc_final: 0.8154 (mttm) REVERT: M 122 TYR cc_start: 0.8089 (t80) cc_final: 0.7465 (t80) REVERT: L 85 GLN cc_start: 0.8692 (tm-30) cc_final: 0.7904 (pt0) REVERT: L 86 LEU cc_start: 0.8682 (mt) cc_final: 0.8335 (mt) REVERT: L 96 LYS cc_start: 0.8607 (tppt) cc_final: 0.8292 (mtmm) outliers start: 39 outliers final: 24 residues processed: 126 average time/residue: 0.1283 time to fit residues: 23.4160 Evaluate side-chains 115 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 60 TRP Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 551 VAL 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 774 ARG 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 873 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain M residue 38 TYR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 96 GLN Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 chunk 9 optimal weight: 0.0030 chunk 17 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 overall best weight: 1.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS ** A 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.113202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.078770 restraints weight = 50682.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.079440 restraints weight = 30584.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.079565 restraints weight = 21790.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.079964 restraints weight = 20605.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.079904 restraints weight = 18278.918| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15064 Z= 0.144 Angle : 0.629 8.417 21642 Z= 0.317 Chirality : 0.036 0.209 2658 Planarity : 0.005 0.053 1784 Dihedral : 23.233 178.020 5378 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.21 % Allowed : 20.56 % Favored : 76.23 % 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: -0.99 (0.26), residues: 1071 helix: 0.78 (0.24), residues: 514 sheet: -1.40 (0.58), residues: 81 loop : -2.20 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 93 TYR 0.019 0.002 TYR A 18 PHE 0.015 0.002 PHE A 345 TRP 0.020 0.001 TRP A 60 HIS 0.009 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00311 (15063) covalent geometry : angle 0.62898 (21642) hydrogen bonds : bond 0.05084 ( 521) hydrogen bonds : angle 3.96029 ( 1322) Misc. bond : bond 0.00027 ( 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 126 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 MET cc_start: 0.5394 (ppp) cc_final: 0.4739 (mmm) REVERT: A 631 ARG cc_start: 0.8494 (ttp-170) cc_final: 0.8246 (ptp-110) REVERT: A 770 GLN cc_start: 0.8741 (mt0) cc_final: 0.8256 (tp-100) REVERT: A 772 TYR cc_start: 0.7091 (t80) cc_final: 0.6015 (m-80) REVERT: A 773 MET cc_start: 0.6331 (ptm) cc_final: 0.6023 (ppp) REVERT: A 774 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7219 (ptt-90) REVERT: M 64 ASN cc_start: 0.8453 (m110) cc_final: 0.8156 (m110) REVERT: M 122 TYR cc_start: 0.8073 (t80) cc_final: 0.7483 (t80) REVERT: L 85 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8027 (pt0) REVERT: L 86 LEU cc_start: 0.8727 (mt) cc_final: 0.8524 (pp) outliers start: 30 outliers final: 24 residues processed: 118 average time/residue: 0.1276 time to fit residues: 21.4063 Evaluate side-chains 114 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 60 TRP Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 551 VAL 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 760 LYS Chi-restraints excluded: chain A residue 774 ARG 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 873 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 940 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 91 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.114000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.079735 restraints weight = 50060.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.080406 restraints weight = 30095.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.080987 restraints weight = 21338.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.081022 restraints weight = 19400.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.080937 restraints weight = 17093.658| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15064 Z= 0.129 Angle : 0.604 8.420 21642 Z= 0.303 Chirality : 0.035 0.202 2658 Planarity : 0.005 0.052 1784 Dihedral : 23.248 177.901 5378 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.00 % Allowed : 21.41 % 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: -0.89 (0.26), residues: 1071 helix: 0.89 (0.24), residues: 517 sheet: -1.24 (0.61), residues: 80 loop : -2.24 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 93 TYR 0.018 0.002 TYR A 18 PHE 0.017 0.002 PHE A 345 TRP 0.020 0.001 TRP A 60 HIS 0.007 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00277 (15063) covalent geometry : angle 0.60403 (21642) hydrogen bonds : bond 0.04782 ( 521) hydrogen bonds : angle 3.87646 ( 1322) Misc. bond : bond 0.00022 ( 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 122 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.6140 (t80) cc_final: 0.5411 (t80) REVERT: A 631 ARG cc_start: 0.8508 (ttp-170) cc_final: 0.8270 (ptp-110) REVERT: A 649 LYS cc_start: 0.7387 (tptp) cc_final: 0.7163 (mmtm) REVERT: A 770 GLN cc_start: 0.8547 (mt0) cc_final: 0.8052 (tp-100) REVERT: A 772 TYR cc_start: 0.7275 (t80) cc_final: 0.6497 (m-80) REVERT: A 774 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8104 (ptt-90) REVERT: M 64 ASN cc_start: 0.8472 (m110) cc_final: 0.8183 (m110) REVERT: M 122 TYR cc_start: 0.8087 (t80) cc_final: 0.7227 (t80) outliers start: 28 outliers final: 23 residues processed: 113 average time/residue: 0.1257 time to fit residues: 20.7904 Evaluate side-chains 110 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 60 TRP Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 551 VAL 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 774 ARG 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 873 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 118 optimal weight: 20.0000 chunk 22 optimal weight: 0.0010 chunk 120 optimal weight: 30.0000 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 0.0270 chunk 6 optimal weight: 0.0010 chunk 96 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.5852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 762 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 = 0.4114 r_free = 0.4114 target = 0.116363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.081989 restraints weight = 50345.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.083039 restraints weight = 29359.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.083278 restraints weight = 20724.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.083822 restraints weight = 19281.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.083808 restraints weight = 17832.911| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15064 Z= 0.107 Angle : 0.587 8.619 21642 Z= 0.292 Chirality : 0.033 0.199 2658 Planarity : 0.004 0.054 1784 Dihedral : 23.205 177.313 5378 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.03 % Allowed : 22.38 % 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: -0.71 (0.26), residues: 1071 helix: 1.08 (0.24), residues: 516 sheet: -1.11 (0.60), residues: 82 loop : -2.19 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 93 TYR 0.015 0.001 TYR L 40 PHE 0.018 0.001 PHE A 345 TRP 0.020 0.001 TRP A 60 HIS 0.005 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00222 (15063) covalent geometry : angle 0.58744 (21642) hydrogen bonds : bond 0.04176 ( 521) hydrogen bonds : angle 3.74418 ( 1322) Misc. bond : bond 0.00059 ( 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 113 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 ARG cc_start: 0.8405 (ttp-170) cc_final: 0.8151 (ptp-110) REVERT: A 649 LYS cc_start: 0.7520 (tptp) cc_final: 0.7173 (mmtm) REVERT: A 770 GLN cc_start: 0.8337 (mt0) cc_final: 0.7958 (tp-100) REVERT: A 772 TYR cc_start: 0.7413 (t80) cc_final: 0.6547 (m-80) REVERT: A 773 MET cc_start: 0.7227 (mmm) cc_final: 0.6512 (tmm) REVERT: M 64 ASN cc_start: 0.8599 (m110) cc_final: 0.8319 (m110) REVERT: L 85 GLN cc_start: 0.8644 (tm-30) cc_final: 0.7888 (pt0) outliers start: 19 outliers final: 19 residues processed: 108 average time/residue: 0.1253 time to fit residues: 19.6235 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 : 0.292 ------------------------------------------------------------------------------- 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 412 HIS Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 676 LEU 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 873 VAL Chi-restraints excluded: chain A residue 898 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 M residue 57 SER Chi-restraints excluded: chain M residue 81 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 chunk 90 optimal weight: 0.0270 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.113059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.077933 restraints weight = 50199.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.078635 restraints weight = 29279.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.079232 restraints weight = 20712.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.079398 restraints weight = 18735.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.079346 restraints weight = 17239.753| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15064 Z= 0.164 Angle : 0.650 8.941 21642 Z= 0.327 Chirality : 0.036 0.249 2658 Planarity : 0.005 0.048 1784 Dihedral : 23.325 176.784 5378 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.36 % Allowed : 23.02 % Favored : 74.63 % 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: -0.91 (0.25), residues: 1071 helix: 0.89 (0.23), residues: 519 sheet: -1.17 (0.59), residues: 82 loop : -2.30 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 78 TYR 0.016 0.002 TYR A 168 PHE 0.019 0.002 PHE A 575 TRP 0.019 0.001 TRP A 60 HIS 0.010 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00356 (15063) covalent geometry : angle 0.65026 (21642) hydrogen bonds : bond 0.05413 ( 521) hydrogen bonds : angle 4.02304 ( 1322) Misc. bond : bond 0.00056 ( 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 108 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 GLN cc_start: 0.7359 (tp40) cc_final: 0.6797 (pp30) REVERT: A 631 ARG cc_start: 0.8518 (ttp-170) cc_final: 0.8267 (ptp-110) REVERT: A 649 LYS cc_start: 0.7339 (tptp) cc_final: 0.7021 (mmtm) REVERT: A 770 GLN cc_start: 0.8475 (mt0) cc_final: 0.7968 (tp-100) REVERT: A 772 TYR cc_start: 0.7462 (t80) cc_final: 0.6425 (m-80) REVERT: M 64 ASN cc_start: 0.8472 (m110) cc_final: 0.8166 (m110) REVERT: L 85 GLN cc_start: 0.8665 (tm-30) cc_final: 0.7880 (pt0) outliers start: 22 outliers final: 20 residues processed: 104 average time/residue: 0.1334 time to fit residues: 19.7215 Evaluate side-chains 102 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 411 THR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 760 LYS 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 873 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 972 ARG 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 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 126 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.113707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.078683 restraints weight = 49779.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.079551 restraints weight = 29045.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.080185 restraints weight = 19756.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.080310 restraints weight = 18662.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.080198 restraints weight = 16827.152| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15064 Z= 0.142 Angle : 0.634 10.358 21642 Z= 0.316 Chirality : 0.035 0.250 2658 Planarity : 0.005 0.066 1784 Dihedral : 23.383 176.975 5378 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.36 % Allowed : 23.13 % 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: -0.79 (0.26), residues: 1071 helix: 0.97 (0.23), residues: 523 sheet: -1.12 (0.61), residues: 81 loop : -2.24 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 93 TYR 0.027 0.002 TYR A 18 PHE 0.015 0.002 PHE A 345 TRP 0.021 0.001 TRP A 60 HIS 0.007 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00309 (15063) covalent geometry : angle 0.63437 (21642) hydrogen bonds : bond 0.04966 ( 521) hydrogen bonds : angle 3.91628 ( 1322) Misc. bond : bond 0.00020 ( 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 105 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 GLN cc_start: 0.7059 (tp40) cc_final: 0.6729 (pp30) REVERT: A 649 LYS cc_start: 0.7379 (tptp) cc_final: 0.7099 (mmtm) REVERT: A 770 GLN cc_start: 0.8363 (mt0) cc_final: 0.7869 (tp-100) REVERT: A 772 TYR cc_start: 0.7307 (t80) cc_final: 0.6531 (m-80) REVERT: M 64 ASN cc_start: 0.8466 (m110) cc_final: 0.8162 (m110) REVERT: M 93 ARG cc_start: 0.8571 (mtm110) cc_final: 0.7880 (ptt-90) outliers start: 22 outliers final: 17 residues processed: 101 average time/residue: 0.1307 time to fit residues: 19.1342 Evaluate side-chains 97 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 412 HIS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 760 LYS 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 873 VAL Chi-restraints excluded: chain A residue 898 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 28 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 114 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 571 ASN A 762 HIS ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.113646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.078356 restraints weight = 49884.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.079672 restraints weight = 28121.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.079908 restraints weight = 18888.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.080108 restraints weight = 19479.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.080002 restraints weight = 17307.779| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15064 Z= 0.138 Angle : 0.628 9.668 21642 Z= 0.313 Chirality : 0.035 0.250 2658 Planarity : 0.005 0.067 1784 Dihedral : 23.383 173.587 5378 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.36 % Allowed : 22.70 % 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: -0.74 (0.26), residues: 1071 helix: 1.02 (0.23), residues: 523 sheet: -1.15 (0.60), residues: 82 loop : -2.21 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG M 93 TYR 0.018 0.002 TYR L 40 PHE 0.015 0.001 PHE A 575 TRP 0.021 0.001 TRP A 60 HIS 0.008 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00301 (15063) covalent geometry : angle 0.62759 (21642) hydrogen bonds : bond 0.04982 ( 521) hydrogen bonds : angle 3.93264 ( 1322) Misc. bond : bond 0.00032 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2466.55 seconds wall clock time: 43 minutes 12.17 seconds (2592.17 seconds total)