Starting phenix.real_space_refine on Wed Jul 30 22:26:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xs7_33423/07_2025/7xs7_33423.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xs7_33423/07_2025/7xs7_33423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xs7_33423/07_2025/7xs7_33423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xs7_33423/07_2025/7xs7_33423.map" model { file = "/net/cci-nas-00/data/ceres_data/7xs7_33423/07_2025/7xs7_33423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xs7_33423/07_2025/7xs7_33423.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 2 5.49 5 S 68 5.16 5 C 8190 2.51 5 N 1908 2.21 5 O 2102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12270 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5867 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 706} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 5867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5867 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 706} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 268 Unusual residues: {'0V9': 1, 'C14': 8, 'D12': 5, 'HP6': 7} Classifications: {'undetermined': 21} Link IDs: {None: 20} Chain: "A" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 268 Unusual residues: {'0V9': 1, 'C14': 8, 'D12': 5, 'HP6': 7} Classifications: {'undetermined': 21} Link IDs: {None: 20} Time building chain proxies: 8.08, per 1000 atoms: 0.66 Number of scatterers: 12270 At special positions: 0 Unit cell: (138.92, 80.04, 115.92, 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 68 16.00 P 2 15.00 O 2102 8.00 N 1908 7.00 C 8190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.5 seconds 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2780 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 6 sheets defined 55.8% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'B' and resid 392 through 401 removed outlier: 3.584A pdb=" N ASP B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 removed outlier: 3.526A pdb=" N LYS B 414 " --> pdb=" O ASN B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.647A pdb=" N LEU B 428 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 478 removed outlier: 3.560A pdb=" N GLY B 463 " --> pdb=" O HIS B 459 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 478 " --> pdb=" O LYS B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 516 removed outlier: 3.562A pdb=" N ALA B 511 " --> pdb=" O GLU B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 removed outlier: 3.591A pdb=" N ALA B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 594 Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 618 through 620 No H-bonds generated for 'chain 'B' and resid 618 through 620' Processing helix chain 'B' and resid 639 through 643 removed outlier: 4.024A pdb=" N LEU B 642 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 643 " --> pdb=" O VAL B 640 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 639 through 643' Processing helix chain 'B' and resid 644 through 660 removed outlier: 4.062A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 669 removed outlier: 3.727A pdb=" N PHE B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 696 removed outlier: 3.556A pdb=" N TYR B 694 " --> pdb=" O PRO B 690 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.633A pdb=" N ASN B 711 " --> pdb=" O PHE B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 716 removed outlier: 3.567A pdb=" N ALA B 715 " --> pdb=" O MET B 712 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 716 " --> pdb=" O TYR B 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 712 through 716' Processing helix chain 'B' and resid 717 through 726 removed outlier: 3.565A pdb=" N CYS B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 725 " --> pdb=" O CYS B 721 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 726 " --> pdb=" O PHE B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 774 removed outlier: 3.605A pdb=" N LEU B 755 " --> pdb=" O PRO B 751 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 756 " --> pdb=" O GLU B 752 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 757 " --> pdb=" O PHE B 753 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN B 762 " --> pdb=" O ARG B 758 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 766 " --> pdb=" O ASN B 762 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER B 768 " --> pdb=" O SER B 764 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 769 " --> pdb=" O PHE B 765 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 771 " --> pdb=" O ALA B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.510A pdb=" N VAL B 778 " --> pdb=" O PHE B 775 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP B 779 " --> pdb=" O TYR B 776 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 780 " --> pdb=" O ARG B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 807 removed outlier: 3.682A pdb=" N LYS B 788 " --> pdb=" O ASN B 784 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE B 799 " --> pdb=" O PHE B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 823 removed outlier: 3.646A pdb=" N PHE B 812 " --> pdb=" O SER B 808 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE B 813 " --> pdb=" O LEU B 809 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 832 removed outlier: 4.088A pdb=" N ASN B 832 " --> pdb=" O SER B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 855 removed outlier: 4.174A pdb=" N LEU B 839 " --> pdb=" O SER B 835 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N CYS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 849 " --> pdb=" O CYS B 845 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE B 850 " --> pdb=" O THR B 846 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 855 " --> pdb=" O ILE B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 896 removed outlier: 4.336A pdb=" N TYR B 865 " --> pdb=" O THR B 861 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 883 " --> pdb=" O MET B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 932 Processing helix chain 'B' and resid 942 through 948 removed outlier: 3.550A pdb=" N ILE B 946 " --> pdb=" O PHE B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 963 removed outlier: 3.782A pdb=" N TYR B 959 " --> pdb=" O VAL B 955 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN B 963 " --> pdb=" O TYR B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1010 Processing helix chain 'B' and resid 1028 through 1037 removed outlier: 3.929A pdb=" N THR B1033 " --> pdb=" O ASP B1029 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY B1034 " --> pdb=" O GLU B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1037 through 1059 removed outlier: 3.526A pdb=" N SER B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL B1043 " --> pdb=" O VAL B1039 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B1044 " --> pdb=" O ARG B1040 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B1045 " --> pdb=" O SER B1041 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B1050 " --> pdb=" O PHE B1046 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN B1051 " --> pdb=" O TRP B1047 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE B1054 " --> pdb=" O THR B1050 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B1055 " --> pdb=" O ASN B1051 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B1058 " --> pdb=" O ILE B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1073 removed outlier: 3.524A pdb=" N TYR B1067 " --> pdb=" O GLY B1063 " (cutoff:3.500A) Processing helix chain 'B' and resid 1092 through 1131 removed outlier: 3.703A pdb=" N ILE B1096 " --> pdb=" O SER B1092 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B1098 " --> pdb=" O ALA B1094 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN B1099 " --> pdb=" O SER B1095 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU B1102 " --> pdb=" O PHE B1098 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B1105 " --> pdb=" O ILE B1101 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B1106 " --> pdb=" O LEU B1102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B1109 " --> pdb=" O VAL B1105 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B1111 " --> pdb=" O LEU B1107 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG B1112 " --> pdb=" O SER B1108 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE B1113 " --> pdb=" O ALA B1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 removed outlier: 3.552A pdb=" N ASP A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.528A pdb=" N LYS A 414 " --> pdb=" O ASN A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.643A pdb=" N LEU A 428 " --> pdb=" O PRO A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 478 removed outlier: 3.555A pdb=" N GLY A 463 " --> pdb=" O HIS A 459 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 removed outlier: 3.981A pdb=" N LYS A 491 " --> pdb=" O ASP A 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 506 through 516 removed outlier: 3.594A pdb=" N ALA A 511 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.590A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 594 Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 639 through 643 removed outlier: 4.039A pdb=" N LEU A 642 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 643 " --> pdb=" O VAL A 640 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 639 through 643' Processing helix chain 'A' and resid 644 through 660 removed outlier: 4.060A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS A 655 " --> pdb=" O ASN A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 669 removed outlier: 3.729A pdb=" N PHE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.561A pdb=" N TYR A 694 " --> pdb=" O PRO A 690 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 711 removed outlier: 3.632A pdb=" N ASN A 711 " --> pdb=" O PHE A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 716 removed outlier: 3.567A pdb=" N ALA A 715 " --> pdb=" O MET A 712 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 716 " --> pdb=" O TYR A 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 712 through 716' Processing helix chain 'A' and resid 717 through 726 removed outlier: 3.570A pdb=" N CYS A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 725 " --> pdb=" O CYS A 721 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 774 removed outlier: 3.553A pdb=" N LEU A 755 " --> pdb=" O PRO A 751 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 757 " --> pdb=" O PHE A 753 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 768 " --> pdb=" O SER A 764 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 769 " --> pdb=" O PHE A 765 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.508A pdb=" N VAL A 778 " --> pdb=" O PHE A 775 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP A 779 " --> pdb=" O TYR A 776 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 780 " --> pdb=" O ARG A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 807 removed outlier: 3.696A pdb=" N LYS A 788 " --> pdb=" O ASN A 784 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 799 " --> pdb=" O PHE A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 823 removed outlier: 3.645A pdb=" N PHE A 812 " --> pdb=" O SER A 808 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 832 removed outlier: 4.089A pdb=" N ASN A 832 " --> pdb=" O SER A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 855 removed outlier: 4.172A pdb=" N LEU A 839 " --> pdb=" O SER A 835 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 849 " --> pdb=" O CYS A 845 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 850 " --> pdb=" O THR A 846 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 855 " --> pdb=" O ILE A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 896 removed outlier: 4.245A pdb=" N TYR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 883 " --> pdb=" O MET A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 932 Processing helix chain 'A' and resid 942 through 948 removed outlier: 3.550A pdb=" N ILE A 946 " --> pdb=" O PHE A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 963 removed outlier: 3.782A pdb=" N TYR A 959 " --> pdb=" O VAL A 955 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 963 " --> pdb=" O TYR A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1012 removed outlier: 3.833A pdb=" N VAL A1011 " --> pdb=" O LYS A1007 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A1012 " --> pdb=" O TYR A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1037 removed outlier: 3.904A pdb=" N THR A1033 " --> pdb=" O ASP A1029 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY A1034 " --> pdb=" O GLU A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1059 removed outlier: 3.527A pdb=" N SER A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL A1043 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A1044 " --> pdb=" O ARG A1040 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A1050 " --> pdb=" O PHE A1046 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A1051 " --> pdb=" O TRP A1047 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE A1054 " --> pdb=" O THR A1050 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A1055 " --> pdb=" O ASN A1051 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A1058 " --> pdb=" O ILE A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1073 removed outlier: 3.525A pdb=" N TYR A1067 " --> pdb=" O GLY A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1131 removed outlier: 3.706A pdb=" N ILE A1096 " --> pdb=" O SER A1092 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A1099 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A1105 " --> pdb=" O ILE A1101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A1109 " --> pdb=" O VAL A1105 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A1111 " --> pdb=" O LEU A1107 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A1112 " --> pdb=" O SER A1108 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A1113 " --> pdb=" O ALA A1109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 386 through 389 removed outlier: 3.558A pdb=" N SER B 389 " --> pdb=" O MET B 416 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLN B 566 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR B 453 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER B 679 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 682 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LYS B 735 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA B 627 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N CYS B 737 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY B 629 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N SER B 739 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N ILE B 631 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N TYR B 741 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 9.915A pdb=" N THR B 633 " --> pdb=" O TYR B 741 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER B 743 " --> pdb=" O THR B 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 386 through 389 removed outlier: 3.558A pdb=" N SER B 389 " --> pdb=" O MET B 416 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N CYS B 570 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE B 497 " --> pdb=" O CYS B 570 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LYS B 572 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N SER B 499 " --> pdb=" O LYS B 572 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR B 453 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER B 679 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 682 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LYS B 735 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA B 627 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N CYS B 737 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY B 629 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N SER B 739 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N ILE B 631 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N TYR B 741 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 9.915A pdb=" N THR B 633 " --> pdb=" O TYR B 741 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER B 743 " --> pdb=" O THR B 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 545 through 549 removed outlier: 3.636A pdb=" N ASN B 545 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU B 557 " --> pdb=" O ASN B 545 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N SER B 555 " --> pdb=" O THR B 547 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 389 removed outlier: 3.516A pdb=" N SER A 389 " --> pdb=" O MET A 416 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLN A 566 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 448 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N CYS A 496 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A 450 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE A 498 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A 452 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR A 453 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A 679 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG A 682 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LYS A 735 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA A 627 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N CYS A 737 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY A 629 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N SER A 739 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N ILE A 631 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N TYR A 741 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N THR A 633 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER A 743 " --> pdb=" O THR A 633 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 389 removed outlier: 3.516A pdb=" N SER A 389 " --> pdb=" O MET A 416 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N CYS A 570 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE A 497 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LYS A 572 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N SER A 499 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 448 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N CYS A 496 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A 450 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE A 498 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A 452 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR A 453 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A 679 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG A 682 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LYS A 735 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA A 627 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N CYS A 737 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY A 629 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N SER A 739 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N ILE A 631 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N TYR A 741 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N THR A 633 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER A 743 " --> pdb=" O THR A 633 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 545 through 549 removed outlier: 3.638A pdb=" N ASN A 545 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 557 " --> pdb=" O ASN A 545 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER A 555 " --> pdb=" O THR A 547 " (cutoff:3.500A) 506 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.33 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1861 1.32 - 1.44: 3439 1.44 - 1.57: 7110 1.57 - 1.69: 4 1.69 - 1.81: 104 Bond restraints: 12518 Sorted by residual: bond pdb=" C1 0V9 B1221 " pdb=" O3P 0V9 B1221 " ideal model delta sigma weight residual 1.409 1.453 -0.044 2.00e-02 2.50e+03 4.87e+00 bond pdb=" C1 0V9 A2001 " pdb=" O3P 0V9 A2001 " ideal model delta sigma weight residual 1.409 1.453 -0.044 2.00e-02 2.50e+03 4.87e+00 bond pdb=" O3P 0V9 B1221 " pdb=" P 0V9 B1221 " ideal model delta sigma weight residual 1.648 1.605 0.043 2.00e-02 2.50e+03 4.53e+00 bond pdb=" C31 0V9 A2001 " pdb=" C32 0V9 A2001 " ideal model delta sigma weight residual 1.535 1.493 0.042 2.00e-02 2.50e+03 4.43e+00 bond pdb=" C31 0V9 B1221 " pdb=" C32 0V9 B1221 " ideal model delta sigma weight residual 1.535 1.493 0.042 2.00e-02 2.50e+03 4.39e+00 ... (remaining 12513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 16219 1.75 - 3.50: 473 3.50 - 5.25: 51 5.25 - 7.00: 8 7.00 - 8.76: 3 Bond angle restraints: 16754 Sorted by residual: angle pdb=" N VAL A 996 " pdb=" CA VAL A 996 " pdb=" C VAL A 996 " ideal model delta sigma weight residual 113.20 107.53 5.67 9.60e-01 1.09e+00 3.49e+01 angle pdb=" N VAL B 996 " pdb=" CA VAL B 996 " pdb=" C VAL B 996 " ideal model delta sigma weight residual 113.20 107.56 5.64 9.60e-01 1.09e+00 3.45e+01 angle pdb=" N ILE B 914 " pdb=" CA ILE B 914 " pdb=" C ILE B 914 " ideal model delta sigma weight residual 112.90 107.85 5.05 9.60e-01 1.09e+00 2.77e+01 angle pdb=" N ILE A 914 " pdb=" CA ILE A 914 " pdb=" C ILE A 914 " ideal model delta sigma weight residual 112.90 107.86 5.04 9.60e-01 1.09e+00 2.75e+01 angle pdb=" N TYR A1028 " pdb=" CA TYR A1028 " pdb=" C TYR A1028 " ideal model delta sigma weight residual 114.56 108.68 5.88 1.27e+00 6.20e-01 2.15e+01 ... (remaining 16749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.57: 7136 27.57 - 55.14: 320 55.14 - 82.71: 24 82.71 - 110.27: 10 110.27 - 137.84: 2 Dihedral angle restraints: 7492 sinusoidal: 3190 harmonic: 4302 Sorted by residual: dihedral pdb=" C37 0V9 A2001 " pdb=" C38 0V9 A2001 " pdb=" C39 0V9 A2001 " pdb=" C40 0V9 A2001 " ideal model delta sinusoidal sigma weight residual 195.15 57.31 137.84 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" C37 0V9 B1221 " pdb=" C38 0V9 B1221 " pdb=" C39 0V9 B1221 " pdb=" C40 0V9 B1221 " ideal model delta sinusoidal sigma weight residual 195.15 57.38 137.77 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" C1 0V9 B1221 " pdb=" O3P 0V9 B1221 " pdb=" P 0V9 B1221 " pdb=" O4P 0V9 B1221 " ideal model delta sinusoidal sigma weight residual -67.07 -170.76 103.69 1 3.00e+01 1.11e-03 1.32e+01 ... (remaining 7489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1015 0.032 - 0.064: 657 0.064 - 0.096: 123 0.096 - 0.128: 38 0.128 - 0.160: 5 Chirality restraints: 1838 Sorted by residual: chirality pdb=" CA ASN A 456 " pdb=" N ASN A 456 " pdb=" C ASN A 456 " pdb=" CB ASN A 456 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA TYR A 538 " pdb=" N TYR A 538 " pdb=" C TYR A 538 " pdb=" CB TYR A 538 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ASN B 456 " pdb=" N ASN B 456 " pdb=" C ASN B 456 " pdb=" CB ASN B 456 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 1835 not shown) Planarity restraints: 2018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 0V9 B1221 " 0.015 2.00e-02 2.50e+03 2.87e-02 8.22e+00 pdb=" C18 0V9 B1221 " -0.038 2.00e-02 2.50e+03 pdb=" C19 0V9 B1221 " 0.038 2.00e-02 2.50e+03 pdb=" C20 0V9 B1221 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 0V9 A2001 " -0.015 2.00e-02 2.50e+03 2.85e-02 8.11e+00 pdb=" C18 0V9 A2001 " 0.037 2.00e-02 2.50e+03 pdb=" C19 0V9 A2001 " -0.037 2.00e-02 2.50e+03 pdb=" C20 0V9 A2001 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A1025 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A1026 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A1026 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1026 " -0.021 5.00e-02 4.00e+02 ... (remaining 2015 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 29 2.54 - 3.13: 8570 3.13 - 3.72: 16280 3.72 - 4.31: 23291 4.31 - 4.90: 40468 Nonbonded interactions: 88638 Sorted by model distance: nonbonded pdb=" O PRO A1026 " pdb=" O SER A1027 " model vdw 1.946 3.040 nonbonded pdb=" O PRO B1026 " pdb=" O SER B1027 " model vdw 1.980 3.040 nonbonded pdb=" OG1 THR B 547 " pdb=" OG SER B 555 " model vdw 2.342 3.040 nonbonded pdb=" OG1 THR A 547 " pdb=" OG SER A 555 " model vdw 2.348 3.040 nonbonded pdb=" O LYS B 981 " pdb=" O ILE B 982 " model vdw 2.371 3.040 ... (remaining 88633 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 378 through 1131 or resid 2002 through 2008 or resid 2010 \ through 2012 or resid 2014 through 2019)) selection = (chain 'B' and (resid 378 through 1131 or resid 1202 through 1208 or resid 1210 \ through 1212 or resid 1214 through 1219)) } 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 individual isotropic 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: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.160 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 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 : 0.004 0.044 12518 Z= 0.222 Angle : 0.710 8.756 16754 Z= 0.442 Chirality : 0.040 0.160 1838 Planarity : 0.003 0.038 2018 Dihedral : 14.805 137.842 4712 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.16 % Favored : 95.56 % Rotamer: Outliers : 0.16 % Allowed : 0.31 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.21), residues: 1442 helix: -1.24 (0.19), residues: 718 sheet: -3.25 (0.32), residues: 134 loop : -2.01 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1103 HIS 0.002 0.001 HIS B 783 PHE 0.013 0.001 PHE B 678 TYR 0.016 0.001 TYR B 538 ARG 0.003 0.000 ARG B 758 Details of bonding type rmsd hydrogen bonds : bond 0.29557 ( 468) hydrogen bonds : angle 7.38437 ( 1464) covalent geometry : bond 0.00434 (12518) covalent geometry : angle 0.71003 (16754) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 1.242 Fit side-chains REVERT: A 1123 ARG cc_start: 0.7152 (ttt90) cc_final: 0.6945 (ttt90) outliers start: 2 outliers final: 0 residues processed: 137 average time/residue: 0.2606 time to fit residues: 51.3376 Evaluate side-chains 106 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 0.0040 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 0.0870 chunk 84 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 overall best weight: 0.5370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 783 HIS B1099 ASN A 560 GLN A 783 HIS A1099 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.092859 restraints weight = 16974.856| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.30 r_work: 0.2830 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12518 Z= 0.112 Angle : 0.480 6.429 16754 Z= 0.257 Chirality : 0.040 0.146 1838 Planarity : 0.003 0.025 2018 Dihedral : 8.898 115.504 2002 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.51 % Favored : 95.35 % Rotamer: Outliers : 0.47 % Allowed : 5.91 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.22), residues: 1442 helix: -0.11 (0.20), residues: 734 sheet: -2.52 (0.36), residues: 134 loop : -1.77 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 806 HIS 0.002 0.001 HIS A 459 PHE 0.016 0.001 PHE A 387 TYR 0.016 0.001 TYR A1028 ARG 0.003 0.000 ARG B 464 Details of bonding type rmsd hydrogen bonds : bond 0.06226 ( 468) hydrogen bonds : angle 4.22146 ( 1464) covalent geometry : bond 0.00220 (12518) covalent geometry : angle 0.47966 (16754) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 1.295 Fit side-chains REVERT: B 457 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.5975 (mp0) REVERT: B 1029 ASP cc_start: 0.8000 (m-30) cc_final: 0.7317 (t0) REVERT: A 457 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.6018 (mp0) REVERT: A 1029 ASP cc_start: 0.7912 (m-30) cc_final: 0.7223 (t0) outliers start: 6 outliers final: 0 residues processed: 127 average time/residue: 0.2263 time to fit residues: 43.0096 Evaluate side-chains 109 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain A residue 457 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 27 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 130 optimal weight: 0.0070 chunk 81 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.123294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.089452 restraints weight = 17221.750| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.32 r_work: 0.2764 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12518 Z= 0.150 Angle : 0.489 9.537 16754 Z= 0.259 Chirality : 0.041 0.156 1838 Planarity : 0.003 0.027 2018 Dihedral : 8.563 92.137 2002 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.13 % Favored : 94.73 % Rotamer: Outliers : 1.48 % Allowed : 8.24 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.22), residues: 1442 helix: 0.40 (0.21), residues: 724 sheet: -2.22 (0.37), residues: 134 loop : -1.81 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 806 HIS 0.003 0.001 HIS A 459 PHE 0.013 0.001 PHE A 678 TYR 0.010 0.001 TYR A 797 ARG 0.002 0.000 ARG A1123 Details of bonding type rmsd hydrogen bonds : bond 0.06318 ( 468) hydrogen bonds : angle 3.91500 ( 1464) covalent geometry : bond 0.00353 (12518) covalent geometry : angle 0.48902 (16754) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 1.283 Fit side-chains REVERT: B 457 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.6094 (mp0) REVERT: B 1029 ASP cc_start: 0.8332 (m-30) cc_final: 0.7640 (t0) REVERT: A 457 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6068 (mp0) REVERT: A 1029 ASP cc_start: 0.8219 (m-30) cc_final: 0.7544 (t0) outliers start: 19 outliers final: 6 residues processed: 125 average time/residue: 0.2205 time to fit residues: 41.7088 Evaluate side-chains 118 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1006 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 35 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.125682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.091911 restraints weight = 16900.466| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.29 r_work: 0.2812 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12518 Z= 0.100 Angle : 0.439 10.120 16754 Z= 0.230 Chirality : 0.039 0.137 1838 Planarity : 0.003 0.025 2018 Dihedral : 8.022 81.432 2002 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.23 % Favored : 95.63 % Rotamer: Outliers : 1.09 % Allowed : 8.79 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1442 helix: 0.79 (0.21), residues: 726 sheet: -1.94 (0.38), residues: 134 loop : -1.69 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 806 HIS 0.002 0.000 HIS A 459 PHE 0.009 0.001 PHE A 678 TYR 0.007 0.001 TYR A 797 ARG 0.003 0.000 ARG B1123 Details of bonding type rmsd hydrogen bonds : bond 0.04926 ( 468) hydrogen bonds : angle 3.56321 ( 1464) covalent geometry : bond 0.00216 (12518) covalent geometry : angle 0.43892 (16754) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: B 379 LYS cc_start: 0.6843 (tppt) cc_final: 0.6122 (tptt) REVERT: B 457 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.6290 (mp0) REVERT: B 1008 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.7851 (m-80) REVERT: B 1029 ASP cc_start: 0.8303 (m-30) cc_final: 0.7677 (t0) REVERT: A 379 LYS cc_start: 0.6848 (tppt) cc_final: 0.6137 (tptt) REVERT: A 457 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.6274 (mp0) REVERT: A 1014 ASP cc_start: 0.7491 (p0) cc_final: 0.7272 (p0) REVERT: A 1029 ASP cc_start: 0.8221 (m-30) cc_final: 0.7542 (t0) outliers start: 14 outliers final: 5 residues processed: 127 average time/residue: 0.2611 time to fit residues: 49.3568 Evaluate side-chains 119 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 967 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 75 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 106 optimal weight: 0.0570 chunk 8 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 131 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.088299 restraints weight = 17193.079| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.33 r_work: 0.2749 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12518 Z= 0.173 Angle : 0.488 7.569 16754 Z= 0.259 Chirality : 0.041 0.140 1838 Planarity : 0.003 0.027 2018 Dihedral : 8.795 83.008 2002 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.34 % Favored : 94.52 % Rotamer: Outliers : 1.48 % Allowed : 10.19 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1442 helix: 0.80 (0.21), residues: 728 sheet: -1.72 (0.39), residues: 134 loop : -1.73 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 806 HIS 0.004 0.001 HIS A 459 PHE 0.014 0.001 PHE A 678 TYR 0.011 0.001 TYR A 797 ARG 0.003 0.000 ARG A 594 Details of bonding type rmsd hydrogen bonds : bond 0.06330 ( 468) hydrogen bonds : angle 3.75865 ( 1464) covalent geometry : bond 0.00419 (12518) covalent geometry : angle 0.48842 (16754) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.928 Fit side-chains REVERT: B 379 LYS cc_start: 0.6983 (tppt) cc_final: 0.6285 (tptt) REVERT: B 457 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.6188 (mp0) REVERT: B 1008 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: B 1029 ASP cc_start: 0.8431 (m-30) cc_final: 0.7777 (t0) REVERT: B 1101 ILE cc_start: 0.9054 (tp) cc_final: 0.8585 (tp) REVERT: A 379 LYS cc_start: 0.6971 (tppt) cc_final: 0.6278 (tptt) REVERT: A 457 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.6259 (mp0) REVERT: A 1014 ASP cc_start: 0.7498 (p0) cc_final: 0.7235 (p0) REVERT: A 1029 ASP cc_start: 0.8406 (m-30) cc_final: 0.7686 (t0) outliers start: 19 outliers final: 11 residues processed: 129 average time/residue: 0.2258 time to fit residues: 43.8644 Evaluate side-chains 124 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1006 ASP Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1039 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 6 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 143 optimal weight: 0.0870 chunk 103 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 overall best weight: 1.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.122127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.087936 restraints weight = 17266.036| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.32 r_work: 0.2742 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12518 Z= 0.167 Angle : 0.484 7.032 16754 Z= 0.258 Chirality : 0.041 0.141 1838 Planarity : 0.003 0.028 2018 Dihedral : 9.039 83.219 2002 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.58 % Favored : 95.28 % Rotamer: Outliers : 1.56 % Allowed : 10.81 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.22), residues: 1442 helix: 0.89 (0.21), residues: 728 sheet: -1.46 (0.42), residues: 134 loop : -1.71 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 806 HIS 0.004 0.001 HIS A 459 PHE 0.014 0.001 PHE A 678 TYR 0.010 0.001 TYR A 797 ARG 0.003 0.000 ARG A1123 Details of bonding type rmsd hydrogen bonds : bond 0.06200 ( 468) hydrogen bonds : angle 3.74061 ( 1464) covalent geometry : bond 0.00402 (12518) covalent geometry : angle 0.48426 (16754) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.434 Fit side-chains REVERT: B 379 LYS cc_start: 0.7052 (tppt) cc_final: 0.6442 (tptt) REVERT: B 457 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.6272 (mp0) REVERT: B 1008 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: B 1029 ASP cc_start: 0.8531 (m-30) cc_final: 0.7898 (t0) REVERT: B 1101 ILE cc_start: 0.9071 (tp) cc_final: 0.8591 (tp) REVERT: A 379 LYS cc_start: 0.7021 (tppt) cc_final: 0.6431 (tptt) REVERT: A 457 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.6227 (mp0) REVERT: A 1006 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8378 (m-30) REVERT: A 1014 ASP cc_start: 0.7495 (p0) cc_final: 0.7226 (p0) REVERT: A 1029 ASP cc_start: 0.8505 (m-30) cc_final: 0.7757 (t0) outliers start: 20 outliers final: 10 residues processed: 126 average time/residue: 0.2598 time to fit residues: 47.2786 Evaluate side-chains 118 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1102 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.087243 restraints weight = 17122.599| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.30 r_work: 0.2725 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12518 Z= 0.184 Angle : 0.500 6.655 16754 Z= 0.267 Chirality : 0.042 0.140 1838 Planarity : 0.003 0.028 2018 Dihedral : 9.534 83.227 2002 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.41 % Favored : 94.45 % Rotamer: Outliers : 2.02 % Allowed : 10.65 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1442 helix: 0.93 (0.20), residues: 728 sheet: -1.28 (0.43), residues: 134 loop : -1.74 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 806 HIS 0.004 0.001 HIS A 459 PHE 0.013 0.001 PHE B 678 TYR 0.010 0.001 TYR B 797 ARG 0.004 0.000 ARG B1123 Details of bonding type rmsd hydrogen bonds : bond 0.06512 ( 468) hydrogen bonds : angle 3.76033 ( 1464) covalent geometry : bond 0.00446 (12518) covalent geometry : angle 0.50021 (16754) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 1.327 Fit side-chains REVERT: B 379 LYS cc_start: 0.6921 (tppt) cc_final: 0.6293 (tptt) REVERT: B 430 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8390 (mt-10) REVERT: B 457 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.6279 (mp0) REVERT: B 1008 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: B 1029 ASP cc_start: 0.8593 (m-30) cc_final: 0.7967 (t0) REVERT: B 1101 ILE cc_start: 0.9103 (tp) cc_final: 0.8608 (tp) REVERT: A 379 LYS cc_start: 0.6972 (tppt) cc_final: 0.6328 (tptt) REVERT: A 457 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.6293 (mp0) REVERT: A 1006 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8359 (m-30) REVERT: A 1014 ASP cc_start: 0.7595 (p0) cc_final: 0.7336 (p0) REVERT: A 1029 ASP cc_start: 0.8550 (m-30) cc_final: 0.7824 (t0) REVERT: A 1101 ILE cc_start: 0.9076 (tp) cc_final: 0.8581 (tp) outliers start: 26 outliers final: 14 residues processed: 129 average time/residue: 0.2483 time to fit residues: 47.9464 Evaluate side-chains 124 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 419 GLN Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1006 ASP Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1102 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 67 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 87 optimal weight: 0.0170 chunk 75 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.122181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.087928 restraints weight = 17259.646| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.34 r_work: 0.2724 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12518 Z= 0.153 Angle : 0.472 6.621 16754 Z= 0.252 Chirality : 0.041 0.140 1838 Planarity : 0.003 0.028 2018 Dihedral : 9.364 82.900 2002 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.79 % Favored : 95.08 % Rotamer: Outliers : 2.26 % Allowed : 10.58 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.23), residues: 1442 helix: 0.99 (0.20), residues: 740 sheet: -1.15 (0.43), residues: 134 loop : -1.80 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 806 HIS 0.004 0.001 HIS A 540 PHE 0.011 0.001 PHE B 678 TYR 0.009 0.001 TYR A 797 ARG 0.005 0.000 ARG B1123 Details of bonding type rmsd hydrogen bonds : bond 0.06016 ( 468) hydrogen bonds : angle 3.64893 ( 1464) covalent geometry : bond 0.00367 (12518) covalent geometry : angle 0.47224 (16754) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.364 Fit side-chains REVERT: B 379 LYS cc_start: 0.6765 (tppt) cc_final: 0.6071 (tptt) REVERT: B 457 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6104 (mp0) REVERT: B 1008 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: B 1029 ASP cc_start: 0.8405 (m-30) cc_final: 0.7855 (t0) REVERT: B 1101 ILE cc_start: 0.9034 (tp) cc_final: 0.8512 (tp) REVERT: A 379 LYS cc_start: 0.6757 (tppt) cc_final: 0.6058 (tptt) REVERT: A 457 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.6107 (mp0) REVERT: A 1006 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8301 (m-30) REVERT: A 1008 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: A 1014 ASP cc_start: 0.7600 (p0) cc_final: 0.7381 (p0) REVERT: A 1029 ASP cc_start: 0.8360 (m-30) cc_final: 0.7724 (t0) REVERT: A 1101 ILE cc_start: 0.9033 (tp) cc_final: 0.8529 (tp) outliers start: 29 outliers final: 14 residues processed: 133 average time/residue: 0.2527 time to fit residues: 49.4165 Evaluate side-chains 123 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 419 GLN Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1008 TYR Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1102 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 0.0270 chunk 67 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.126458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.092819 restraints weight = 16929.516| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.22 r_work: 0.2792 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12518 Z= 0.091 Angle : 0.421 6.471 16754 Z= 0.223 Chirality : 0.039 0.137 1838 Planarity : 0.003 0.028 2018 Dihedral : 8.358 82.308 2002 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.92 % Favored : 94.94 % Rotamer: Outliers : 1.48 % Allowed : 11.20 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.23), residues: 1442 helix: 1.40 (0.21), residues: 736 sheet: -1.04 (0.44), residues: 134 loop : -1.65 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1103 HIS 0.003 0.000 HIS A 540 PHE 0.007 0.001 PHE A 678 TYR 0.007 0.001 TYR A 842 ARG 0.005 0.000 ARG B1123 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 468) hydrogen bonds : angle 3.28316 ( 1464) covalent geometry : bond 0.00190 (12518) covalent geometry : angle 0.42065 (16754) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.288 Fit side-chains REVERT: B 379 LYS cc_start: 0.6826 (tppt) cc_final: 0.6185 (tptt) REVERT: B 457 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.6443 (mp0) REVERT: B 1002 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7435 (tm-30) REVERT: B 1008 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.7878 (m-80) REVERT: B 1029 ASP cc_start: 0.8530 (m-30) cc_final: 0.7927 (t0) REVERT: A 379 LYS cc_start: 0.6808 (tppt) cc_final: 0.6172 (tptt) REVERT: A 457 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.6449 (mp0) REVERT: A 1002 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7187 (tm-30) REVERT: A 1006 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8189 (m-30) REVERT: A 1014 ASP cc_start: 0.7515 (p0) cc_final: 0.7244 (p0) REVERT: A 1029 ASP cc_start: 0.8470 (m-30) cc_final: 0.7747 (t0) outliers start: 19 outliers final: 11 residues processed: 126 average time/residue: 0.2408 time to fit residues: 44.4642 Evaluate side-chains 121 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 1 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 112 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 64 optimal weight: 0.0970 chunk 140 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.092878 restraints weight = 16852.666| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.21 r_work: 0.2775 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12518 Z= 0.092 Angle : 0.424 7.722 16754 Z= 0.224 Chirality : 0.039 0.135 1838 Planarity : 0.003 0.027 2018 Dihedral : 8.252 81.809 2002 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.51 % Favored : 95.35 % Rotamer: Outliers : 1.17 % Allowed : 11.66 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.23), residues: 1442 helix: 1.54 (0.21), residues: 738 sheet: -0.91 (0.44), residues: 134 loop : -1.58 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 806 HIS 0.003 0.001 HIS A 540 PHE 0.007 0.001 PHE A 678 TYR 0.007 0.001 TYR A 842 ARG 0.004 0.000 ARG B1123 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 468) hydrogen bonds : angle 3.23624 ( 1464) covalent geometry : bond 0.00201 (12518) covalent geometry : angle 0.42399 (16754) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 1.321 Fit side-chains REVERT: B 379 LYS cc_start: 0.6858 (tppt) cc_final: 0.6287 (tptt) REVERT: B 457 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.6395 (mp0) REVERT: B 1002 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7386 (tm-30) REVERT: B 1008 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7932 (m-80) REVERT: B 1029 ASP cc_start: 0.8531 (m-30) cc_final: 0.7943 (t0) REVERT: A 457 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.6401 (mp0) REVERT: A 1002 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7194 (tm-30) REVERT: A 1006 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8211 (m-30) REVERT: A 1014 ASP cc_start: 0.7477 (p0) cc_final: 0.7181 (p0) REVERT: A 1029 ASP cc_start: 0.8463 (m-30) cc_final: 0.7764 (t0) outliers start: 15 outliers final: 11 residues processed: 125 average time/residue: 0.2375 time to fit residues: 44.3706 Evaluate side-chains 124 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 8 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.125211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.091095 restraints weight = 16941.901| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.27 r_work: 0.2762 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12518 Z= 0.120 Angle : 0.456 7.416 16754 Z= 0.241 Chirality : 0.040 0.137 1838 Planarity : 0.003 0.027 2018 Dihedral : 8.437 82.102 2002 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.06 % Favored : 94.80 % Rotamer: Outliers : 1.24 % Allowed : 11.98 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.23), residues: 1442 helix: 1.51 (0.21), residues: 742 sheet: -0.78 (0.44), residues: 134 loop : -1.56 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 806 HIS 0.003 0.001 HIS A 540 PHE 0.010 0.001 PHE A 378 TYR 0.008 0.001 TYR B 797 ARG 0.004 0.000 ARG B1123 Details of bonding type rmsd hydrogen bonds : bond 0.04936 ( 468) hydrogen bonds : angle 3.34940 ( 1464) covalent geometry : bond 0.00281 (12518) covalent geometry : angle 0.45587 (16754) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5945.11 seconds wall clock time: 103 minutes 51.10 seconds (6231.10 seconds total)