Starting phenix.real_space_refine on Wed Mar 4 10:12:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xs7_33423/03_2026/7xs7_33423.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xs7_33423/03_2026/7xs7_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 { model { file = "/net/cci-nas-00/data/ceres_data/7xs7_33423/03_2026/7xs7_33423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xs7_33423/03_2026/7xs7_33423.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xs7_33423/03_2026/7xs7_33423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xs7_33423/03_2026/7xs7_33423.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'PHE: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: {'ASN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'PHE: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: 2.88, per 1000 atoms: 0.23 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: 0.91 Conformation dependent library (CDL) restraints added in 560.5 milliseconds 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: 0.47 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: 2.24 Time building geometry restraints manager: 1.22 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: 0.02 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: 2.860 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: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.400 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.310 ------------------------------------------------------------------------------- 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 : 3.99 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (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 ARG 0.003 0.000 ARG B 758 TYR 0.016 0.001 TYR B 538 PHE 0.013 0.001 PHE B 678 TRP 0.007 0.001 TRP B1103 HIS 0.002 0.001 HIS B 783 Details of bonding type rmsd covalent geometry : bond 0.00434 (12518) covalent geometry : angle 0.71003 (16754) hydrogen bonds : bond 0.29557 ( 468) hydrogen bonds : angle 7.38437 ( 1464) *********************** 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 : 0.353 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: 0.1092 time to fit residues: 21.6346 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 : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0050 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.0170 overall best weight: 0.7434 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.125492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.091734 restraints weight = 17104.789| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.31 r_work: 0.2795 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1242 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= 0.118 Angle : 0.489 6.379 16754 Z= 0.263 Chirality : 0.040 0.147 1838 Planarity : 0.003 0.026 2018 Dihedral : 9.169 118.228 2002 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.72 % Favored : 95.15 % Rotamer: Outliers : 0.54 % Allowed : 5.60 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.22), residues: 1442 helix: -0.08 (0.20), residues: 732 sheet: -2.52 (0.36), residues: 134 loop : -1.80 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 464 TYR 0.015 0.001 TYR A1028 PHE 0.017 0.001 PHE A 387 TRP 0.006 0.001 TRP A 806 HIS 0.003 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00239 (12518) covalent geometry : angle 0.48883 (16754) hydrogen bonds : bond 0.06575 ( 468) hydrogen bonds : angle 4.28994 ( 1464) *********************** 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 125 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.407 Fit side-chains REVERT: B 457 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.6168 (mp0) REVERT: B 656 MET cc_start: 0.8992 (mmp) cc_final: 0.8782 (mmp) REVERT: B 1029 ASP cc_start: 0.8271 (m-30) cc_final: 0.7495 (t0) REVERT: A 457 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.6155 (mp0) REVERT: A 656 MET cc_start: 0.9014 (mmp) cc_final: 0.8808 (mmp) REVERT: A 1029 ASP cc_start: 0.8169 (m-30) cc_final: 0.7379 (t0) outliers start: 7 outliers final: 1 residues processed: 121 average time/residue: 0.1033 time to fit residues: 18.5323 Evaluate side-chains 108 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 105 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 1006 ASP 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 33 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.120994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.087040 restraints weight = 17308.480| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.32 r_work: 0.2724 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12518 Z= 0.218 Angle : 0.549 9.188 16754 Z= 0.292 Chirality : 0.043 0.162 1838 Planarity : 0.003 0.030 2018 Dihedral : 9.634 93.604 2002 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.34 % Favored : 94.52 % Rotamer: Outliers : 1.40 % Allowed : 8.55 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.22), residues: 1442 helix: 0.24 (0.20), residues: 724 sheet: -2.22 (0.38), residues: 134 loop : -1.87 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 912 TYR 0.015 0.002 TYR B 538 PHE 0.017 0.001 PHE A 678 TRP 0.017 0.001 TRP A 806 HIS 0.004 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00533 (12518) covalent geometry : angle 0.54904 (16754) hydrogen bonds : bond 0.07372 ( 468) hydrogen bonds : angle 4.14757 ( 1464) *********************** 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 129 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.365 Fit side-chains REVERT: B 457 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.6142 (mp0) REVERT: B 1008 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7719 (m-80) REVERT: B 1029 ASP cc_start: 0.8465 (m-30) cc_final: 0.7742 (t0) REVERT: A 457 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.6126 (mp0) REVERT: A 1008 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: A 1029 ASP cc_start: 0.8400 (m-30) cc_final: 0.7630 (t0) outliers start: 18 outliers final: 5 residues processed: 124 average time/residue: 0.0991 time to fit residues: 18.7576 Evaluate side-chains 117 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 1008 TYR Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1008 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 130 optimal weight: 30.0000 chunk 20 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.088390 restraints weight = 17156.597| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.31 r_work: 0.2752 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12518 Z= 0.156 Angle : 0.488 7.365 16754 Z= 0.259 Chirality : 0.041 0.145 1838 Planarity : 0.003 0.029 2018 Dihedral : 9.296 83.969 2002 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.58 % Favored : 95.28 % Rotamer: Outliers : 1.17 % Allowed : 9.95 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.22), residues: 1442 helix: 0.52 (0.21), residues: 728 sheet: -1.93 (0.39), residues: 134 loop : -1.88 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1123 TYR 0.010 0.001 TYR A 797 PHE 0.017 0.001 PHE A 387 TRP 0.011 0.001 TRP A 806 HIS 0.004 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00371 (12518) covalent geometry : angle 0.48805 (16754) hydrogen bonds : bond 0.06307 ( 468) hydrogen bonds : angle 3.87291 ( 1464) *********************** 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 130 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.440 Fit side-chains REVERT: B 379 LYS cc_start: 0.6988 (tppt) cc_final: 0.6346 (tptt) REVERT: B 457 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.6280 (mp0) REVERT: B 1008 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: B 1014 ASP cc_start: 0.7568 (p0) cc_final: 0.7351 (p0) REVERT: B 1029 ASP cc_start: 0.8498 (m-30) cc_final: 0.7751 (t0) REVERT: B 1101 ILE cc_start: 0.9056 (tp) cc_final: 0.8580 (tp) REVERT: A 379 LYS cc_start: 0.6974 (tppt) cc_final: 0.6340 (tptt) REVERT: A 457 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.6263 (mp0) REVERT: A 1008 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: A 1014 ASP cc_start: 0.7556 (p0) cc_final: 0.7354 (p0) REVERT: A 1029 ASP cc_start: 0.8388 (m-30) cc_final: 0.7655 (t0) REVERT: A 1101 ILE cc_start: 0.9049 (tp) cc_final: 0.8577 (tp) outliers start: 15 outliers final: 9 residues processed: 127 average time/residue: 0.1102 time to fit residues: 20.6252 Evaluate side-chains 119 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 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 1008 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.088542 restraints weight = 17214.443| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.33 r_work: 0.2745 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12518 Z= 0.141 Angle : 0.470 10.748 16754 Z= 0.249 Chirality : 0.041 0.141 1838 Planarity : 0.003 0.028 2018 Dihedral : 9.013 83.337 2002 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.27 % Favored : 94.59 % Rotamer: Outliers : 1.63 % Allowed : 10.65 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.22), residues: 1442 helix: 0.76 (0.21), residues: 728 sheet: -1.73 (0.40), residues: 134 loop : -1.82 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1123 TYR 0.009 0.001 TYR B 797 PHE 0.011 0.001 PHE A 678 TRP 0.012 0.001 TRP A 806 HIS 0.003 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00334 (12518) covalent geometry : angle 0.47028 (16754) hydrogen bonds : bond 0.05875 ( 468) hydrogen bonds : angle 3.70668 ( 1464) *********************** 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 134 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.438 Fit side-chains REVERT: B 379 LYS cc_start: 0.7091 (tppt) cc_final: 0.6419 (tptt) REVERT: B 457 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.6285 (mp0) REVERT: B 1008 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.7765 (m-80) REVERT: B 1014 ASP cc_start: 0.7554 (p0) cc_final: 0.7294 (p0) REVERT: B 1029 ASP cc_start: 0.8537 (m-30) cc_final: 0.7805 (t0) REVERT: A 379 LYS cc_start: 0.7081 (tppt) cc_final: 0.6419 (tptt) REVERT: A 457 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.6193 (mp0) REVERT: A 1006 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8347 (m-30) REVERT: A 1014 ASP cc_start: 0.7585 (p0) cc_final: 0.7339 (p0) REVERT: A 1029 ASP cc_start: 0.8436 (m-30) cc_final: 0.7699 (t0) REVERT: A 1101 ILE cc_start: 0.9041 (tp) cc_final: 0.8559 (tp) outliers start: 21 outliers final: 12 residues processed: 131 average time/residue: 0.1090 time to fit residues: 20.9880 Evaluate side-chains 124 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 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 45 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.089794 restraints weight = 16918.840| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.29 r_work: 0.2754 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12518 Z= 0.118 Angle : 0.443 8.281 16754 Z= 0.236 Chirality : 0.040 0.139 1838 Planarity : 0.003 0.027 2018 Dihedral : 8.666 82.795 2002 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.30 % Favored : 95.56 % Rotamer: Outliers : 1.63 % Allowed : 11.43 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.23), residues: 1442 helix: 1.01 (0.21), residues: 732 sheet: -1.48 (0.42), residues: 134 loop : -1.74 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1123 TYR 0.008 0.001 TYR B 797 PHE 0.010 0.001 PHE A 678 TRP 0.010 0.001 TRP A 806 HIS 0.003 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00270 (12518) covalent geometry : angle 0.44268 (16754) hydrogen bonds : bond 0.05337 ( 468) hydrogen bonds : angle 3.52862 ( 1464) *********************** 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 128 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.322 Fit side-chains REVERT: B 379 LYS cc_start: 0.6997 (tppt) cc_final: 0.6354 (tptt) REVERT: B 457 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.6258 (mp0) REVERT: B 1014 ASP cc_start: 0.7511 (p0) cc_final: 0.7243 (p0) REVERT: B 1029 ASP cc_start: 0.8562 (m-30) cc_final: 0.7866 (t0) REVERT: A 379 LYS cc_start: 0.7010 (tppt) cc_final: 0.6373 (tptt) REVERT: A 457 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.6208 (mp0) REVERT: A 1014 ASP cc_start: 0.7533 (p0) cc_final: 0.7268 (p0) REVERT: A 1029 ASP cc_start: 0.8421 (m-30) cc_final: 0.7710 (t0) outliers start: 21 outliers final: 11 residues processed: 125 average time/residue: 0.1021 time to fit residues: 18.6703 Evaluate side-chains 117 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 436 ARG 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 1039 VAL Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1039 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 134 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.119823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.085914 restraints weight = 17314.815| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.29 r_work: 0.2696 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12518 Z= 0.247 Angle : 0.548 7.701 16754 Z= 0.293 Chirality : 0.044 0.147 1838 Planarity : 0.003 0.029 2018 Dihedral : 10.158 83.514 2002 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.62 % Favored : 94.24 % Rotamer: Outliers : 2.10 % Allowed : 11.28 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.22), residues: 1442 helix: 0.71 (0.20), residues: 732 sheet: -1.21 (0.43), residues: 134 loop : -1.76 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 436 TYR 0.012 0.002 TYR A 418 PHE 0.016 0.002 PHE A 678 TRP 0.016 0.002 TRP B 806 HIS 0.004 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00610 (12518) covalent geometry : angle 0.54809 (16754) hydrogen bonds : bond 0.07383 ( 468) hydrogen bonds : angle 3.93791 ( 1464) *********************** 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 142 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.448 Fit side-chains REVERT: B 379 LYS cc_start: 0.6966 (tppt) cc_final: 0.6317 (tptt) REVERT: B 430 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8353 (mt-10) REVERT: B 457 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: B 480 LYS cc_start: 0.8603 (mmmm) cc_final: 0.8367 (mmmt) REVERT: B 1101 ILE cc_start: 0.9117 (tp) cc_final: 0.8606 (tp) REVERT: A 379 LYS cc_start: 0.6929 (tppt) cc_final: 0.6306 (tptt) REVERT: A 457 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.6346 (mp0) REVERT: A 480 LYS cc_start: 0.8611 (mmmm) cc_final: 0.8349 (mmmt) REVERT: A 1006 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8395 (m-30) REVERT: A 1014 ASP cc_start: 0.7687 (p0) cc_final: 0.7439 (p0) REVERT: A 1029 ASP cc_start: 0.8611 (m-30) cc_final: 0.7890 (t0) REVERT: A 1101 ILE cc_start: 0.9114 (tp) cc_final: 0.8611 (tp) outliers start: 27 outliers final: 13 residues processed: 138 average time/residue: 0.0976 time to fit residues: 20.0292 Evaluate side-chains 125 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 967 LEU Chi-restraints excluded: chain B residue 1006 ASP Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1128 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 Chi-restraints excluded: chain A residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 138 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 131 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.122851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.089021 restraints weight = 16931.592| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.29 r_work: 0.2726 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12518 Z= 0.125 Angle : 0.452 7.638 16754 Z= 0.241 Chirality : 0.040 0.142 1838 Planarity : 0.003 0.029 2018 Dihedral : 9.186 82.905 2002 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.51 % Favored : 95.35 % Rotamer: Outliers : 1.71 % Allowed : 11.74 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.23), residues: 1442 helix: 0.99 (0.21), residues: 744 sheet: -1.12 (0.44), residues: 134 loop : -1.81 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1123 TYR 0.008 0.001 TYR A 842 PHE 0.010 0.001 PHE A 678 TRP 0.010 0.001 TRP A 806 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00287 (12518) covalent geometry : angle 0.45154 (16754) hydrogen bonds : bond 0.05460 ( 468) hydrogen bonds : angle 3.54815 ( 1464) *********************** 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 132 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.416 Fit side-chains REVERT: B 379 LYS cc_start: 0.6833 (tppt) cc_final: 0.6194 (tptt) REVERT: B 430 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8326 (mt-10) REVERT: B 457 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.6309 (mp0) REVERT: B 1029 ASP cc_start: 0.8690 (m-30) cc_final: 0.7850 (t0) REVERT: B 1101 ILE cc_start: 0.9064 (tp) cc_final: 0.8557 (tp) REVERT: A 379 LYS cc_start: 0.6825 (tppt) cc_final: 0.6180 (tptt) REVERT: A 457 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.6246 (mp0) REVERT: A 1002 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7208 (tm-30) REVERT: A 1006 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8206 (m-30) REVERT: A 1014 ASP cc_start: 0.7626 (p0) cc_final: 0.7371 (p0) REVERT: A 1029 ASP cc_start: 0.8534 (m-30) cc_final: 0.7794 (t0) REVERT: A 1101 ILE cc_start: 0.9066 (tp) cc_final: 0.8547 (tp) outliers start: 22 outliers final: 15 residues processed: 131 average time/residue: 0.1007 time to fit residues: 19.4483 Evaluate side-chains 125 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 508 ARG 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 948 LEU Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 948 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 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 35 optimal weight: 0.8980 chunk 89 optimal weight: 0.3980 chunk 143 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 140 optimal weight: 0.0050 chunk 43 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.126611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.093039 restraints weight = 16781.381| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.20 r_work: 0.2797 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2330 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= 0.088 Angle : 0.423 10.322 16754 Z= 0.221 Chirality : 0.039 0.136 1838 Planarity : 0.003 0.028 2018 Dihedral : 8.218 81.792 2002 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.58 % Favored : 95.28 % Rotamer: Outliers : 1.09 % Allowed : 12.29 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.23), residues: 1442 helix: 1.46 (0.21), residues: 734 sheet: -0.99 (0.44), residues: 134 loop : -1.68 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1123 TYR 0.007 0.001 TYR A 842 PHE 0.007 0.001 PHE A 678 TRP 0.008 0.001 TRP A1103 HIS 0.003 0.000 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00189 (12518) covalent geometry : angle 0.42339 (16754) hydrogen bonds : bond 0.04102 ( 468) hydrogen bonds : angle 3.22890 ( 1464) *********************** 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 131 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.436 Fit side-chains REVERT: B 379 LYS cc_start: 0.6889 (tppt) cc_final: 0.6275 (tptt) REVERT: B 457 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.6410 (mp0) REVERT: B 1002 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7411 (tm-30) REVERT: B 1029 ASP cc_start: 0.8626 (m-30) cc_final: 0.7826 (t0) REVERT: B 1101 ILE cc_start: 0.9008 (tp) cc_final: 0.8492 (tp) REVERT: A 379 LYS cc_start: 0.6884 (tppt) cc_final: 0.6270 (tptt) REVERT: A 457 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.6402 (mp0) REVERT: A 1002 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7199 (tm-30) REVERT: A 1006 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8207 (m-30) REVERT: A 1014 ASP cc_start: 0.7511 (p0) cc_final: 0.7246 (p0) REVERT: A 1029 ASP cc_start: 0.8494 (m-30) cc_final: 0.7768 (t0) REVERT: A 1101 ILE cc_start: 0.9011 (tp) cc_final: 0.8487 (tp) outliers start: 14 outliers final: 11 residues processed: 128 average time/residue: 0.1018 time to fit residues: 19.2465 Evaluate side-chains 121 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 508 ARG 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 1039 VAL Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 457 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 135 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.124683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.090778 restraints weight = 16978.575| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.28 r_work: 0.2782 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12518 Z= 0.114 Angle : 0.444 8.994 16754 Z= 0.235 Chirality : 0.040 0.139 1838 Planarity : 0.003 0.028 2018 Dihedral : 8.395 81.999 2002 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.37 % Favored : 95.49 % Rotamer: Outliers : 1.17 % Allowed : 12.60 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.23), residues: 1442 helix: 1.47 (0.21), residues: 740 sheet: -0.86 (0.44), residues: 134 loop : -1.61 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1123 TYR 0.008 0.001 TYR A 842 PHE 0.010 0.001 PHE B1113 TRP 0.011 0.001 TRP B 806 HIS 0.003 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00263 (12518) covalent geometry : angle 0.44445 (16754) hydrogen bonds : bond 0.04890 ( 468) hydrogen bonds : angle 3.33532 ( 1464) ********************** 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 128 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.396 Fit side-chains REVERT: B 379 LYS cc_start: 0.6883 (tppt) cc_final: 0.6246 (tptt) REVERT: B 457 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.6396 (mp0) REVERT: B 1002 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7417 (tm-30) REVERT: B 1029 ASP cc_start: 0.8646 (m-30) cc_final: 0.7875 (t0) REVERT: B 1101 ILE cc_start: 0.9038 (tp) cc_final: 0.8515 (tp) REVERT: A 379 LYS cc_start: 0.6776 (tppt) cc_final: 0.6134 (tptt) REVERT: A 457 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.6311 (mp0) REVERT: A 1002 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7225 (tm-30) REVERT: A 1006 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8225 (m-30) REVERT: A 1014 ASP cc_start: 0.7515 (p0) cc_final: 0.7238 (p0) REVERT: A 1029 ASP cc_start: 0.8508 (m-30) cc_final: 0.7837 (t0) REVERT: A 1101 ILE cc_start: 0.9026 (tp) cc_final: 0.8488 (tp) outliers start: 15 outliers final: 12 residues processed: 126 average time/residue: 0.1053 time to fit residues: 19.5387 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 : 0.427 ------------------------------------------------------------------------------- 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 508 ARG 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 1039 VAL Chi-restraints excluded: chain A residue 380 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 Chi-restraints excluded: chain A residue 1039 VAL 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 7 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 68 optimal weight: 0.0030 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 overall best weight: 1.1396 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.124488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.090577 restraints weight = 16842.580| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.28 r_work: 0.2790 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12518 Z= 0.114 Angle : 0.442 9.063 16754 Z= 0.234 Chirality : 0.040 0.138 1838 Planarity : 0.003 0.027 2018 Dihedral : 8.469 82.092 2002 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.72 % Favored : 95.15 % Rotamer: Outliers : 1.63 % Allowed : 12.21 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.23), residues: 1442 helix: 1.49 (0.21), residues: 740 sheet: -0.73 (0.45), residues: 134 loop : -1.57 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1123 TYR 0.008 0.001 TYR A 797 PHE 0.010 0.001 PHE A1113 TRP 0.010 0.001 TRP A 806 HIS 0.003 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00264 (12518) covalent geometry : angle 0.44217 (16754) hydrogen bonds : bond 0.04997 ( 468) hydrogen bonds : angle 3.36481 ( 1464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2810.32 seconds wall clock time: 48 minutes 51.18 seconds (2931.18 seconds total)