Starting phenix.real_space_refine on Sat Aug 23 12:59:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gv9_34288/08_2025/8gv9_34288.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gv9_34288/08_2025/8gv9_34288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gv9_34288/08_2025/8gv9_34288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gv9_34288/08_2025/8gv9_34288.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gv9_34288/08_2025/8gv9_34288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gv9_34288/08_2025/8gv9_34288.map" } resolution = 3.06 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= -0.001 sd= 0.152 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 S 60 5.16 5 Cl 2 4.86 5 C 7964 2.51 5 N 2046 2.21 5 O 2098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12170 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6084 Classifications: {'peptide': 766} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 38, 'TRANS': 727} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 6084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6084 Classifications: {'peptide': 766} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 38, 'TRANS': 727} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.27, per 1000 atoms: 0.19 Number of scatterers: 12170 At special positions: 0 Unit cell: (91.3, 127.6, 123.2, 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) Cl 2 17.00 S 60 16.00 O 2098 8.00 N 2046 7.00 C 7964 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: 0.78 Conformation dependent library (CDL) restraints added in 473.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2892 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 7 sheets defined 60.4% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 393 through 407 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 415 through 424 Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 568 through 580 Processing helix chain 'A' and resid 582 through 591 removed outlier: 3.944A pdb=" N TYR A 590 " --> pdb=" O HIS A 586 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 607 removed outlier: 3.916A pdb=" N LEU A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 607 " --> pdb=" O ASN A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 641 removed outlier: 4.088A pdb=" N SER A 625 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 632 " --> pdb=" O HIS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 693 Processing helix chain 'A' and resid 694 through 696 No H-bonds generated for 'chain 'A' and resid 694 through 696' Processing helix chain 'A' and resid 697 through 702 removed outlier: 3.674A pdb=" N ASP A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 734 removed outlier: 4.234A pdb=" N LEU A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A 710 " --> pdb=" O PRO A 706 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A 721 " --> pdb=" O PHE A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix Processing helix chain 'A' and resid 739 through 758 Processing helix chain 'A' and resid 768 through 785 Processing helix chain 'A' and resid 788 through 810 removed outlier: 3.654A pdb=" N GLY A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG A 793 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL A 794 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP A 795 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 802 " --> pdb=" O PHE A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 819 removed outlier: 4.296A pdb=" N PHE A 814 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 816 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 819 " --> pdb=" O VAL A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 850 removed outlier: 3.505A pdb=" N GLN A 824 " --> pdb=" O SER A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 923 removed outlier: 3.960A pdb=" N LEU A 903 " --> pdb=" O ASN A 899 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN A 923 " --> pdb=" O ARG A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 937 Processing helix chain 'A' and resid 938 through 954 removed outlier: 3.554A pdb=" N ILE A 954 " --> pdb=" O VAL A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 996 removed outlier: 3.722A pdb=" N MET A 994 " --> pdb=" O PRO A 990 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1020 removed outlier: 3.791A pdb=" N LEU A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A1004 " --> pdb=" O PRO A1000 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1046 removed outlier: 4.203A pdb=" N LEU A1036 " --> pdb=" O PHE A1032 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A1037 " --> pdb=" O HIS A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1067 Processing helix chain 'A' and resid 1091 through 1102 Processing helix chain 'A' and resid 1106 through 1111 Processing helix chain 'A' and resid 1114 through 1129 removed outlier: 3.941A pdb=" N LEU A1118 " --> pdb=" O PRO A1114 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A1129 " --> pdb=" O MET A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1141 Processing helix chain 'A' and resid 1142 through 1144 No H-bonds generated for 'chain 'A' and resid 1142 through 1144' Processing helix chain 'A' and resid 1145 through 1149 removed outlier: 3.570A pdb=" N HIS A1149 " --> pdb=" O PRO A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1157 removed outlier: 4.006A pdb=" N LYS A1157 " --> pdb=" O THR A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1183 removed outlier: 3.639A pdb=" N THR A1183 " --> pdb=" O ALA A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1187 No H-bonds generated for 'chain 'A' and resid 1185 through 1187' Processing helix chain 'A' and resid 1188 through 1195 removed outlier: 3.549A pdb=" N ILE A1192 " --> pdb=" O ALA A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1208 removed outlier: 3.675A pdb=" N LEU A1199 " --> pdb=" O LEU A1195 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A1204 " --> pdb=" O ARG A1200 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR A1205 " --> pdb=" O MET A1201 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A1206 " --> pdb=" O VAL A1202 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A1207 " --> pdb=" O VAL A1203 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 381 removed outlier: 3.842A pdb=" N ALA B 381 " --> pdb=" O ARG B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 408 Processing helix chain 'B' and resid 415 through 424 Processing helix chain 'B' and resid 500 through 510 removed outlier: 3.636A pdb=" N GLU B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 509 " --> pdb=" O LYS B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 580 Processing helix chain 'B' and resid 582 through 591 removed outlier: 3.793A pdb=" N LEU B 591 " --> pdb=" O GLU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 607 removed outlier: 3.536A pdb=" N THR B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 601 " --> pdb=" O ASP B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 641 removed outlier: 3.920A pdb=" N GLN B 630 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG B 631 " --> pdb=" O ALA B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 693 Processing helix chain 'B' and resid 695 through 700 removed outlier: 4.059A pdb=" N ASP B 699 " --> pdb=" O HIS B 695 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE B 700 " --> pdb=" O TYR B 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 695 through 700' Processing helix chain 'B' and resid 705 through 734 removed outlier: 3.580A pdb=" N LEU B 709 " --> pdb=" O ASP B 705 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 712 " --> pdb=" O CYS B 708 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE B 713 " --> pdb=" O LEU B 709 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE B 714 " --> pdb=" O ALA B 710 " (cutoff:3.500A) Proline residue: B 722 - end of helix Processing helix chain 'B' and resid 739 through 758 removed outlier: 3.674A pdb=" N VAL B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE B 754 " --> pdb=" O GLN B 750 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS B 755 " --> pdb=" O GLY B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 784 Processing helix chain 'B' and resid 788 through 810 removed outlier: 3.925A pdb=" N GLY B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG B 793 " --> pdb=" O TYR B 789 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL B 794 " --> pdb=" O LEU B 790 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TRP B 795 " --> pdb=" O VAL B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 819 Processing helix chain 'B' and resid 820 through 850 removed outlier: 3.859A pdb=" N ILE B 826 " --> pdb=" O PHE B 822 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B 848 " --> pdb=" O VAL B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 923 removed outlier: 3.504A pdb=" N LEU B 903 " --> pdb=" O ASN B 899 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 915 " --> pdb=" O THR B 911 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE B 917 " --> pdb=" O PHE B 913 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 918 " --> pdb=" O ILE B 914 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 921 " --> pdb=" O PHE B 917 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN B 923 " --> pdb=" O ARG B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 937 Processing helix chain 'B' and resid 938 through 954 removed outlier: 3.543A pdb=" N ILE B 942 " --> pdb=" O PHE B 938 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 954 " --> pdb=" O VAL B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1020 removed outlier: 3.557A pdb=" N ALA B1001 " --> pdb=" O SER B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1047 removed outlier: 3.574A pdb=" N LEU B1037 " --> pdb=" O HIS B1033 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B1047 " --> pdb=" O GLY B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1050 No H-bonds generated for 'chain 'B' and resid 1048 through 1050' Processing helix chain 'B' and resid 1057 through 1067 Processing helix chain 'B' and resid 1091 through 1102 Processing helix chain 'B' and resid 1109 through 1113 removed outlier: 3.767A pdb=" N GLN B1112 " --> pdb=" O LEU B1109 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B1113 " --> pdb=" O LEU B1110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1109 through 1113' Processing helix chain 'B' and resid 1114 through 1129 removed outlier: 3.913A pdb=" N LEU B1118 " --> pdb=" O PRO B1114 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1141 Processing helix chain 'B' and resid 1145 through 1149 removed outlier: 3.654A pdb=" N HIS B1149 " --> pdb=" O PRO B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1157 removed outlier: 3.969A pdb=" N LYS B1157 " --> pdb=" O THR B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1182 removed outlier: 3.660A pdb=" N SER B1182 " --> pdb=" O TRP B1178 " (cutoff:3.500A) Processing helix chain 'B' and resid 1188 through 1208 Proline residue: B1198 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 350 through 352 removed outlier: 5.293A pdb=" N GLU A 342 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLU A 329 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 344 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N CYS A 523 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N ALA A 514 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N PHE A 555 " --> pdb=" O ALA A 514 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA A 516 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N PHE A 557 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 518 " --> pdb=" O PHE A 557 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU A 559 " --> pdb=" O VAL A 518 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 520 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLY A 561 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY A 522 " --> pdb=" O GLY A 561 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHE A 555 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N GLU A 539 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 12.346A pdb=" N PHE A 557 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 12.371A pdb=" N LEU A 537 " --> pdb=" O PHE A 557 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU A 559 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 12.866A pdb=" N VAL A 535 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 11.497A pdb=" N GLY A 561 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 12.490A pdb=" N ALA A 533 " --> pdb=" O GLY A 561 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL A 385 " --> pdb=" O PHE A 534 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ARG A 536 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU A 387 " --> pdb=" O ARG A 536 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ARG A 538 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU A 389 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ALA A 540 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 352 removed outlier: 6.367A pdb=" N TRP A 340 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 369 removed outlier: 3.603A pdb=" N VAL B 610 " --> pdb=" O LEU A 612 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 610 " --> pdb=" O LEU B 612 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1069 through 1071 removed outlier: 6.973A pdb=" N VAL A1070 " --> pdb=" O GLN A1084 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 350 through 352 removed outlier: 6.926A pdb=" N LEU B 327 " --> pdb=" O THR B 343 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG B 345 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B 325 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N CYS B 523 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ALA B 516 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE B 555 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY B 561 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG B 554 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 556 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG B 538 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 352 removed outlier: 6.476A pdb=" N TRP B 340 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1069 through 1071 removed outlier: 7.105A pdb=" N VAL B1070 " --> pdb=" O GLN B1084 " (cutoff:3.500A) 629 hydrogen bonds defined for protein. 1842 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: 1.93 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3861 1.34 - 1.46: 1894 1.46 - 1.57: 6586 1.57 - 1.69: 1 1.69 - 1.81: 102 Bond restraints: 12444 Sorted by residual: bond pdb=" CA LEU B 591 " pdb=" C LEU B 591 " ideal model delta sigma weight residual 1.528 1.579 -0.051 1.04e-02 9.25e+03 2.36e+01 bond pdb=" CA ASN A 923 " pdb=" C ASN A 923 " ideal model delta sigma weight residual 1.522 1.561 -0.039 1.37e-02 5.33e+03 8.08e+00 bond pdb=" C GLN B 336 " pdb=" N GLU B 337 " ideal model delta sigma weight residual 1.330 1.367 -0.037 1.47e-02 4.63e+03 6.26e+00 bond pdb=" CA ARG B 930 " pdb=" C ARG B 930 " ideal model delta sigma weight residual 1.524 1.551 -0.026 1.28e-02 6.10e+03 4.25e+00 bond pdb=" CA LEU B 843 " pdb=" C LEU B 843 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.35e-02 5.49e+03 3.98e+00 ... (remaining 12439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 16503 1.94 - 3.89: 279 3.89 - 5.83: 60 5.83 - 7.78: 23 7.78 - 9.72: 5 Bond angle restraints: 16870 Sorted by residual: angle pdb=" N ILE B 931 " pdb=" CA ILE B 931 " pdb=" C ILE B 931 " ideal model delta sigma weight residual 110.62 118.74 -8.12 1.02e+00 9.61e-01 6.34e+01 angle pdb=" N VAL B 844 " pdb=" CA VAL B 844 " pdb=" C VAL B 844 " ideal model delta sigma weight residual 110.72 103.33 7.39 1.01e+00 9.80e-01 5.35e+01 angle pdb=" N LYS B 842 " pdb=" CA LYS B 842 " pdb=" C LYS B 842 " ideal model delta sigma weight residual 111.07 118.61 -7.54 1.07e+00 8.73e-01 4.97e+01 angle pdb=" N PHE B1135 " pdb=" CA PHE B1135 " pdb=" C PHE B1135 " ideal model delta sigma weight residual 114.62 106.69 7.93 1.14e+00 7.69e-01 4.83e+01 angle pdb=" N LEU B 806 " pdb=" CA LEU B 806 " pdb=" C LEU B 806 " ideal model delta sigma weight residual 111.28 118.21 -6.93 1.09e+00 8.42e-01 4.05e+01 ... (remaining 16865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6499 17.97 - 35.94: 755 35.94 - 53.92: 173 53.92 - 71.89: 21 71.89 - 89.86: 18 Dihedral angle restraints: 7466 sinusoidal: 3024 harmonic: 4442 Sorted by residual: dihedral pdb=" CA ARG B 624 " pdb=" C ARG B 624 " pdb=" N SER B 625 " pdb=" CA SER B 625 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA SER A 625 " pdb=" C SER A 625 " pdb=" N VAL A 626 " pdb=" CA VAL A 626 " ideal model delta harmonic sigma weight residual -180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CB GLU A1212 " pdb=" CG GLU A1212 " pdb=" CD GLU A1212 " pdb=" OE1 GLU A1212 " ideal model delta sinusoidal sigma weight residual 0.00 89.64 -89.64 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1691 0.061 - 0.122: 256 0.122 - 0.183: 21 0.183 - 0.244: 6 0.244 - 0.305: 4 Chirality restraints: 1978 Sorted by residual: chirality pdb=" CA LYS B 842 " pdb=" N LYS B 842 " pdb=" C LYS B 842 " pdb=" CB LYS B 842 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA TYR B 590 " pdb=" N TYR B 590 " pdb=" C TYR B 590 " pdb=" CB TYR B 590 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA LEU B 591 " pdb=" N LEU B 591 " pdb=" C LEU B 591 " pdb=" CB LEU B 591 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1975 not shown) Planarity restraints: 2110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 394 " 0.055 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO A 395 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 395 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 395 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 394 " -0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO B 395 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 395 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 395 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 510 " 0.048 5.00e-02 4.00e+02 7.21e-02 8.31e+00 pdb=" N PRO A 511 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " 0.039 5.00e-02 4.00e+02 ... (remaining 2107 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 60 2.60 - 3.18: 9792 3.18 - 3.75: 17282 3.75 - 4.33: 23625 4.33 - 4.90: 41144 Nonbonded interactions: 91903 Sorted by model distance: nonbonded pdb=" O ASN B 785 " pdb=" OD1 ASN B 785 " model vdw 2.028 3.040 nonbonded pdb=" O LEU A 730 " pdb=" OG1 THR A 734 " model vdw 2.085 3.040 nonbonded pdb=" O LEU B 591 " pdb=" CD1 LEU B 591 " model vdw 2.141 3.460 nonbonded pdb=" O ALA B1076 " pdb=" OD1 ASP B1079 " model vdw 2.161 3.040 nonbonded pdb=" OE2 GLU A 350 " pdb=" OD1 ASP A 352 " model vdw 2.189 3.040 ... (remaining 91898 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' selection = chain 'B' } 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: 1.080 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: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 9.800 Find NCS groups from input model: 0.290 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 0.072 12444 Z= 0.168 Angle : 0.686 9.725 16870 Z= 0.431 Chirality : 0.046 0.305 1978 Planarity : 0.005 0.082 2110 Dihedral : 16.238 89.859 4574 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.01 % Favored : 94.79 % Rotamer: Outliers : 0.23 % Allowed : 15.04 % Favored : 84.74 % 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 aren not related in a simple way. whole: -0.09 (0.22), residues: 1516 helix: 0.72 (0.18), residues: 842 sheet: 0.48 (0.44), residues: 114 loop : -1.33 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 624 TYR 0.007 0.001 TYR B1154 PHE 0.019 0.001 PHE A1189 TRP 0.010 0.001 TRP B 340 HIS 0.006 0.001 HIS B 586 Details of bonding type rmsd covalent geometry : bond 0.00360 (12444) covalent geometry : angle 0.68585 (16870) hydrogen bonds : bond 0.18140 ( 625) hydrogen bonds : angle 5.26480 ( 1842) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 175 time to evaluate : 0.385 Fit side-chains REVERT: B 1196 THR cc_start: 0.7948 (t) cc_final: 0.7719 (p) outliers start: 3 outliers final: 2 residues processed: 176 average time/residue: 0.0964 time to fit residues: 24.3103 Evaluate side-chains 168 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain B residue 323 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 853 HIS B 853 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.170096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.131192 restraints weight = 13025.044| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.33 r_work: 0.3221 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12444 Z= 0.165 Angle : 0.578 9.645 16870 Z= 0.300 Chirality : 0.042 0.161 1978 Planarity : 0.005 0.060 2110 Dihedral : 4.257 30.526 1645 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.01 % Favored : 94.79 % Rotamer: Outliers : 1.95 % Allowed : 16.62 % Favored : 81.43 % 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 aren not related in a simple way. whole: 0.06 (0.22), residues: 1516 helix: 0.89 (0.18), residues: 862 sheet: 0.62 (0.47), residues: 110 loop : -1.44 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 624 TYR 0.009 0.001 TYR A 789 PHE 0.020 0.002 PHE A 822 TRP 0.011 0.001 TRP A 340 HIS 0.009 0.001 HIS B 586 Details of bonding type rmsd covalent geometry : bond 0.00392 (12444) covalent geometry : angle 0.57849 (16870) hydrogen bonds : bond 0.06786 ( 625) hydrogen bonds : angle 4.19249 ( 1842) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.497 Fit side-chains REVERT: A 697 LEU cc_start: 0.8617 (mm) cc_final: 0.8354 (mm) REVERT: A 1156 LYS cc_start: 0.8336 (mtpt) cc_final: 0.7789 (mptt) REVERT: B 321 HIS cc_start: 0.6597 (OUTLIER) cc_final: 0.6300 (m-70) REVERT: B 1156 LYS cc_start: 0.8150 (mtpt) cc_final: 0.7561 (mptt) outliers start: 26 outliers final: 17 residues processed: 194 average time/residue: 0.1165 time to fit residues: 32.3281 Evaluate side-chains 189 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1205 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 129 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 HIS B 853 HIS B 899 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.164449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.125018 restraints weight = 13278.161| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.21 r_work: 0.3103 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12444 Z= 0.225 Angle : 0.631 6.650 16870 Z= 0.327 Chirality : 0.045 0.174 1978 Planarity : 0.006 0.055 2110 Dihedral : 4.398 25.114 1642 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.47 % Favored : 94.33 % Rotamer: Outliers : 3.91 % Allowed : 15.94 % Favored : 80.15 % 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 aren not related in a simple way. whole: -0.27 (0.21), residues: 1516 helix: 0.57 (0.18), residues: 876 sheet: 0.64 (0.47), residues: 110 loop : -1.58 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 624 TYR 0.013 0.002 TYR A 789 PHE 0.024 0.002 PHE A1189 TRP 0.016 0.002 TRP B 340 HIS 0.009 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00562 (12444) covalent geometry : angle 0.63082 (16870) hydrogen bonds : bond 0.07700 ( 625) hydrogen bonds : angle 4.24853 ( 1842) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 182 time to evaluate : 0.535 Fit side-chains REVERT: A 586 HIS cc_start: 0.7856 (OUTLIER) cc_final: 0.6872 (p-80) REVERT: A 697 LEU cc_start: 0.8689 (mm) cc_final: 0.8474 (mm) REVERT: A 1156 LYS cc_start: 0.8394 (mtpt) cc_final: 0.7826 (mptt) REVERT: B 743 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7651 (mp) REVERT: B 762 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8331 (mp) REVERT: B 981 ASN cc_start: 0.8676 (p0) cc_final: 0.8364 (p0) REVERT: B 1141 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7867 (mp) REVERT: B 1156 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7645 (mptt) outliers start: 52 outliers final: 35 residues processed: 219 average time/residue: 0.1154 time to fit residues: 36.4986 Evaluate side-chains 217 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1137 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1196 THR Chi-restraints excluded: chain B residue 1205 THR Chi-restraints excluded: chain B residue 1215 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 75 optimal weight: 0.0370 chunk 131 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 HIS ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 HIS B 899 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.170808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.130095 restraints weight = 13045.024| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.29 r_work: 0.3178 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12444 Z= 0.112 Angle : 0.491 6.167 16870 Z= 0.257 Chirality : 0.039 0.140 1978 Planarity : 0.004 0.053 2110 Dihedral : 4.048 20.891 1642 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.42 % Favored : 95.45 % Rotamer: Outliers : 3.23 % Allowed : 16.99 % Favored : 79.77 % 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 aren not related in a simple way. whole: 0.24 (0.22), residues: 1516 helix: 1.06 (0.18), residues: 874 sheet: 0.79 (0.48), residues: 110 loop : -1.51 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 624 TYR 0.007 0.001 TYR A 569 PHE 0.019 0.001 PHE A1189 TRP 0.008 0.001 TRP A 346 HIS 0.008 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00241 (12444) covalent geometry : angle 0.49069 (16870) hydrogen bonds : bond 0.05249 ( 625) hydrogen bonds : angle 3.91867 ( 1842) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 0.463 Fit side-chains REVERT: A 697 LEU cc_start: 0.8630 (mm) cc_final: 0.8414 (mm) REVERT: A 1085 GLU cc_start: 0.8043 (pt0) cc_final: 0.7757 (pt0) REVERT: A 1156 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7763 (mptt) REVERT: B 586 HIS cc_start: 0.7307 (OUTLIER) cc_final: 0.6961 (p90) REVERT: B 590 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.6082 (t80) REVERT: B 981 ASN cc_start: 0.8482 (p0) cc_final: 0.8163 (p0) REVERT: B 1156 LYS cc_start: 0.8115 (mtpt) cc_final: 0.7579 (mptt) outliers start: 43 outliers final: 30 residues processed: 205 average time/residue: 0.1164 time to fit residues: 33.7941 Evaluate side-chains 195 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1196 THR Chi-restraints excluded: chain B residue 1215 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 48 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 0.0870 chunk 113 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 HIS B 853 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.165119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123605 restraints weight = 13289.646| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.44 r_work: 0.3105 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12444 Z= 0.197 Angle : 0.583 6.200 16870 Z= 0.302 Chirality : 0.043 0.163 1978 Planarity : 0.005 0.053 2110 Dihedral : 4.233 24.430 1642 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.41 % Favored : 94.46 % Rotamer: Outliers : 4.29 % Allowed : 16.47 % Favored : 79.25 % 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 aren not related in a simple way. whole: -0.01 (0.22), residues: 1516 helix: 0.82 (0.18), residues: 876 sheet: 0.72 (0.47), residues: 110 loop : -1.54 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 624 TYR 0.011 0.002 TYR A 789 PHE 0.022 0.002 PHE B1189 TRP 0.013 0.001 TRP B 340 HIS 0.008 0.001 HIS B 586 Details of bonding type rmsd covalent geometry : bond 0.00488 (12444) covalent geometry : angle 0.58283 (16870) hydrogen bonds : bond 0.07023 ( 625) hydrogen bonds : angle 4.05101 ( 1842) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 171 time to evaluate : 0.511 Fit side-chains REVERT: A 697 LEU cc_start: 0.8643 (mm) cc_final: 0.8442 (mm) REVERT: A 1156 LYS cc_start: 0.8312 (mtpt) cc_final: 0.7789 (mptt) REVERT: B 586 HIS cc_start: 0.7349 (OUTLIER) cc_final: 0.6952 (p90) REVERT: B 981 ASN cc_start: 0.8444 (p0) cc_final: 0.8079 (p0) REVERT: B 1141 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7842 (mp) REVERT: B 1156 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7588 (mptt) outliers start: 57 outliers final: 46 residues processed: 215 average time/residue: 0.1150 time to fit residues: 36.0811 Evaluate side-chains 217 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 169 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1215 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1196 THR Chi-restraints excluded: chain B residue 1205 THR Chi-restraints excluded: chain B residue 1215 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 132 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 HIS B 785 ASN B 853 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.169983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.127639 restraints weight = 13153.619| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.41 r_work: 0.3126 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12444 Z= 0.123 Angle : 0.500 6.107 16870 Z= 0.260 Chirality : 0.040 0.234 1978 Planarity : 0.004 0.052 2110 Dihedral : 4.045 22.144 1642 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.42 % Favored : 95.45 % Rotamer: Outliers : 4.29 % Allowed : 17.37 % Favored : 78.35 % 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 aren not related in a simple way. whole: 0.30 (0.22), residues: 1516 helix: 1.11 (0.18), residues: 874 sheet: 0.85 (0.47), residues: 110 loop : -1.49 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 624 TYR 0.007 0.001 TYR A 569 PHE 0.019 0.001 PHE A1189 TRP 0.008 0.001 TRP A 340 HIS 0.008 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00281 (12444) covalent geometry : angle 0.49975 (16870) hydrogen bonds : bond 0.05507 ( 625) hydrogen bonds : angle 3.87737 ( 1842) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 168 time to evaluate : 0.457 Fit side-chains REVERT: A 633 MET cc_start: 0.7927 (ttp) cc_final: 0.7718 (ttm) REVERT: A 697 LEU cc_start: 0.8631 (mm) cc_final: 0.8400 (mm) REVERT: A 1085 GLU cc_start: 0.8084 (pt0) cc_final: 0.7838 (pt0) REVERT: A 1156 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7742 (mptt) REVERT: B 586 HIS cc_start: 0.7331 (OUTLIER) cc_final: 0.6931 (p90) REVERT: B 590 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.6088 (t80) REVERT: B 981 ASN cc_start: 0.8514 (p0) cc_final: 0.8177 (p0) REVERT: B 1156 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7542 (mptt) outliers start: 57 outliers final: 44 residues processed: 209 average time/residue: 0.1129 time to fit residues: 34.6945 Evaluate side-chains 210 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 785 ASN Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1196 THR Chi-restraints excluded: chain B residue 1215 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 120 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 3 optimal weight: 0.0670 chunk 117 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 853 HIS B 785 ASN B 853 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.163531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121902 restraints weight = 13213.392| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.45 r_work: 0.3076 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 12444 Z= 0.262 Angle : 0.653 6.456 16870 Z= 0.337 Chirality : 0.047 0.236 1978 Planarity : 0.006 0.053 2110 Dihedral : 4.442 28.528 1642 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.61 % Favored : 94.13 % Rotamer: Outliers : 5.26 % Allowed : 16.84 % Favored : 77.89 % 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 aren not related in a simple way. whole: -0.23 (0.21), residues: 1516 helix: 0.62 (0.18), residues: 876 sheet: 0.64 (0.46), residues: 114 loop : -1.62 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 624 TYR 0.013 0.002 TYR A 789 PHE 0.022 0.002 PHE B1189 TRP 0.016 0.002 TRP B 340 HIS 0.011 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00661 (12444) covalent geometry : angle 0.65271 (16870) hydrogen bonds : bond 0.08000 ( 625) hydrogen bonds : angle 4.19813 ( 1842) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 180 time to evaluate : 0.404 Fit side-chains REVERT: A 1156 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7745 (mptt) REVERT: B 586 HIS cc_start: 0.7573 (OUTLIER) cc_final: 0.7113 (p90) REVERT: B 981 ASN cc_start: 0.8600 (p0) cc_final: 0.8283 (p0) REVERT: B 1141 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8033 (mp) REVERT: B 1156 LYS cc_start: 0.8275 (mtpt) cc_final: 0.7645 (mptt) outliers start: 70 outliers final: 51 residues processed: 233 average time/residue: 0.0969 time to fit residues: 33.4374 Evaluate side-chains 232 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 179 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1215 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 959 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1196 THR Chi-restraints excluded: chain B residue 1205 THR Chi-restraints excluded: chain B residue 1215 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 118 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 99 optimal weight: 0.0170 chunk 13 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 HIS A 853 HIS B 785 ASN B 853 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.167139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125535 restraints weight = 13050.228| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.37 r_work: 0.3105 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12444 Z= 0.133 Angle : 0.518 6.305 16870 Z= 0.270 Chirality : 0.041 0.182 1978 Planarity : 0.005 0.055 2110 Dihedral : 4.164 25.574 1642 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.49 % Favored : 95.38 % Rotamer: Outliers : 3.83 % Allowed : 18.12 % Favored : 78.05 % 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 aren not related in a simple way. whole: 0.17 (0.22), residues: 1516 helix: 0.99 (0.18), residues: 876 sheet: 0.86 (0.48), residues: 110 loop : -1.52 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 701 TYR 0.007 0.001 TYR A 569 PHE 0.019 0.001 PHE A1189 TRP 0.010 0.001 TRP B 340 HIS 0.008 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00307 (12444) covalent geometry : angle 0.51768 (16870) hydrogen bonds : bond 0.05779 ( 625) hydrogen bonds : angle 3.93431 ( 1842) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 176 time to evaluate : 0.399 Fit side-chains REVERT: A 633 MET cc_start: 0.7976 (ttp) cc_final: 0.7749 (ttm) REVERT: A 1156 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7765 (mptt) REVERT: B 586 HIS cc_start: 0.7282 (OUTLIER) cc_final: 0.6926 (p90) REVERT: B 981 ASN cc_start: 0.8459 (p0) cc_final: 0.8154 (p0) REVERT: B 1156 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7563 (mptt) outliers start: 51 outliers final: 48 residues processed: 214 average time/residue: 0.1076 time to fit residues: 33.3729 Evaluate side-chains 221 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1215 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 785 ASN Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1196 THR Chi-restraints excluded: chain B residue 1215 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 39 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 HIS B 785 ASN B 853 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.167964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.126330 restraints weight = 13070.945| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.33 r_work: 0.3109 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12444 Z= 0.153 Angle : 0.543 11.473 16870 Z= 0.280 Chirality : 0.042 0.180 1978 Planarity : 0.005 0.054 2110 Dihedral : 4.143 26.290 1642 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.28 % Favored : 94.59 % Rotamer: Outliers : 4.44 % Allowed : 17.52 % Favored : 78.05 % 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 aren not related in a simple way. whole: 0.22 (0.22), residues: 1516 helix: 1.02 (0.18), residues: 876 sheet: 0.90 (0.48), residues: 110 loop : -1.50 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 701 TYR 0.008 0.001 TYR B 789 PHE 0.021 0.002 PHE A1189 TRP 0.011 0.001 TRP B 340 HIS 0.008 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00366 (12444) covalent geometry : angle 0.54286 (16870) hydrogen bonds : bond 0.06133 ( 625) hydrogen bonds : angle 3.93113 ( 1842) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 176 time to evaluate : 0.462 Fit side-chains REVERT: A 633 MET cc_start: 0.8015 (ttp) cc_final: 0.7787 (ttm) REVERT: A 1156 LYS cc_start: 0.8319 (mtpt) cc_final: 0.7784 (mptt) REVERT: B 586 HIS cc_start: 0.7294 (OUTLIER) cc_final: 0.6931 (p90) REVERT: B 981 ASN cc_start: 0.8486 (p0) cc_final: 0.8196 (p0) REVERT: B 1141 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7829 (mp) REVERT: B 1156 LYS cc_start: 0.8256 (mtpt) cc_final: 0.7679 (mptt) outliers start: 59 outliers final: 52 residues processed: 223 average time/residue: 0.0908 time to fit residues: 29.9333 Evaluate side-chains 227 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 173 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1215 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 785 ASN Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1196 THR Chi-restraints excluded: chain B residue 1215 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 108 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 HIS B 785 ASN B 853 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.164848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122944 restraints weight = 13221.182| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.35 r_work: 0.3057 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12444 Z= 0.244 Angle : 0.637 7.838 16870 Z= 0.329 Chirality : 0.046 0.207 1978 Planarity : 0.006 0.055 2110 Dihedral : 4.407 30.761 1642 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.87 % Favored : 94.00 % Rotamer: Outliers : 4.36 % Allowed : 17.97 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.16 (0.21), residues: 1516 helix: 0.70 (0.18), residues: 876 sheet: 0.66 (0.47), residues: 114 loop : -1.61 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 701 TYR 0.012 0.002 TYR A 789 PHE 0.023 0.002 PHE B1189 TRP 0.014 0.002 TRP B 340 HIS 0.010 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00615 (12444) covalent geometry : angle 0.63701 (16870) hydrogen bonds : bond 0.07634 ( 625) hydrogen bonds : angle 4.14208 ( 1842) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 179 time to evaluate : 0.458 Fit side-chains REVERT: A 1156 LYS cc_start: 0.8313 (mtpt) cc_final: 0.7793 (mptt) REVERT: B 586 HIS cc_start: 0.7509 (OUTLIER) cc_final: 0.7076 (p90) REVERT: B 983 LEU cc_start: 0.8658 (mt) cc_final: 0.8338 (mt) REVERT: B 1141 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7874 (mp) REVERT: B 1156 LYS cc_start: 0.8326 (mtpt) cc_final: 0.7750 (mptt) outliers start: 58 outliers final: 53 residues processed: 225 average time/residue: 0.1098 time to fit residues: 36.0139 Evaluate side-chains 236 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 181 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1215 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 785 ASN Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1196 THR Chi-restraints excluded: chain B residue 1215 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 17 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 0.0020 chunk 44 optimal weight: 3.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 853 HIS B 785 ASN B 853 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.169252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127110 restraints weight = 13108.883| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.40 r_work: 0.3120 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12444 Z= 0.126 Angle : 0.516 7.501 16870 Z= 0.271 Chirality : 0.040 0.165 1978 Planarity : 0.005 0.055 2110 Dihedral : 4.125 26.930 1642 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.49 % Favored : 95.38 % Rotamer: Outliers : 3.46 % Allowed : 19.17 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.22), residues: 1516 helix: 1.08 (0.18), residues: 876 sheet: 0.93 (0.48), residues: 110 loop : -1.49 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 701 TYR 0.007 0.001 TYR A 569 PHE 0.019 0.001 PHE A1189 TRP 0.011 0.001 TRP A 340 HIS 0.009 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00285 (12444) covalent geometry : angle 0.51579 (16870) hydrogen bonds : bond 0.05597 ( 625) hydrogen bonds : angle 3.89750 ( 1842) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2794.99 seconds wall clock time: 48 minutes 31.60 seconds (2911.60 seconds total)