Starting phenix.real_space_refine on Thu Mar 5 10:44:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x2a_21999/03_2026/6x2a_21999_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x2a_21999/03_2026/6x2a_21999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x2a_21999/03_2026/6x2a_21999_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x2a_21999/03_2026/6x2a_21999_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x2a_21999/03_2026/6x2a_21999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x2a_21999/03_2026/6x2a_21999.map" } resolution = 3.3 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= 0.002 sd= 0.057 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 13803 2.51 5 N 3617 2.21 5 O 4046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21562 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7404 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 47, 'TRANS': 918} Chain breaks: 12 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 10, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 6861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 6861 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 46, 'TRANS': 901} Chain breaks: 13 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 961, 7297 Classifications: {'peptide': 961} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 47, 'TRANS': 913} Chain breaks: 11 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 7, 'ASP:plan': 13, 'GLN:plan1': 3, 'GLU:plan': 13, 'ARG:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 143 Time building chain proxies: 5.23, per 1000 atoms: 0.24 Number of scatterers: 21562 At special positions: 0 Unit cell: (131.192, 135.424, 180.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 4046 8.00 N 3617 7.00 C 13803 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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: 1.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5404 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 47 sheets defined 28.0% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.097A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.684A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.580A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.561A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.209A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 759 removed outlier: 7.045A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 759 " --> pdb=" O TYR A 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 759' Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.758A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.658A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 4.004A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.527A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.517A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.636A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.733A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 removed outlier: 3.690A pdb=" N VAL A1128 " --> pdb=" O ASN A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.403A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.926A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.623A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.645A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.970A pdb=" N GLN B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.974A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 759 removed outlier: 7.077A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 759 " --> pdb=" O TYR B 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 755 through 759' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.799A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.167A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.515A pdb=" N ASP B 820 " --> pdb=" O SER B 816 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.632A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.689A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1129 removed outlier: 3.841A pdb=" N VAL B1128 " --> pdb=" O ASN B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.577A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.053A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.305A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.849A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 759 removed outlier: 7.129A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE C 759 " --> pdb=" O TYR C 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 755 through 759' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.735A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.352A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.534A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 4.168A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.509A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.071A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.356A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE C 587 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.046A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 230 removed outlier: 6.316A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 224 through 230 removed outlier: 6.316A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.327A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.753A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 356 Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.934A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.144A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.578A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.224A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.856A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.831A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.274A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.299A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 645 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 327 removed outlier: 5.628A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.577A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.413A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.093A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.610A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.556A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.747A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.760A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.713A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.608A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.703A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.932A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.866A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.752A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.903A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.625A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2661 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: 5.34 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5567 1.33 - 1.45: 4151 1.45 - 1.57: 12180 1.57 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 22018 Sorted by residual: bond pdb=" CZ ARG B 905 " pdb=" NH2 ARG B 905 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.78e+00 bond pdb=" CZ ARG A1000 " pdb=" NH2 ARG A1000 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.62e+00 bond pdb=" N VAL A 213 " pdb=" CA VAL A 213 " ideal model delta sigma weight residual 1.456 1.485 -0.029 9.50e-03 1.11e+04 9.26e+00 bond pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 9.22e+00 bond pdb=" CZ ARG B 34 " pdb=" NH2 ARG B 34 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.22e+00 ... (remaining 22013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 19885 1.65 - 3.30: 8308 3.30 - 4.95: 1638 4.95 - 6.60: 175 6.60 - 8.25: 19 Bond angle restraints: 30025 Sorted by residual: angle pdb=" CA ASP C 427 " pdb=" CB ASP C 427 " pdb=" CG ASP C 427 " ideal model delta sigma weight residual 112.60 119.46 -6.86 1.00e+00 1.00e+00 4.70e+01 angle pdb=" CA PHE B 275 " pdb=" CB PHE B 275 " pdb=" CG PHE B 275 " ideal model delta sigma weight residual 113.80 119.38 -5.58 1.00e+00 1.00e+00 3.11e+01 angle pdb=" CA ASN B 211 " pdb=" CB ASN B 211 " pdb=" CG ASN B 211 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" CA ASP B 228 " pdb=" CB ASP B 228 " pdb=" CG ASP B 228 " ideal model delta sigma weight residual 112.60 118.10 -5.50 1.00e+00 1.00e+00 3.02e+01 angle pdb=" CA PHE A 329 " pdb=" CB PHE A 329 " pdb=" CG PHE A 329 " ideal model delta sigma weight residual 113.80 119.28 -5.48 1.00e+00 1.00e+00 3.01e+01 ... (remaining 30020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 12218 17.95 - 35.90: 695 35.90 - 53.84: 101 53.84 - 71.79: 45 71.79 - 89.74: 16 Dihedral angle restraints: 13075 sinusoidal: 4725 harmonic: 8350 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 178.46 -85.46 1 1.00e+01 1.00e-02 8.84e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 170.35 -77.35 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 170.00 -77.00 1 1.00e+01 1.00e-02 7.44e+01 ... (remaining 13072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2391 0.086 - 0.171: 987 0.171 - 0.257: 129 0.257 - 0.342: 21 0.342 - 0.428: 5 Chirality restraints: 3533 Sorted by residual: chirality pdb=" CA ASP C 571 " pdb=" N ASP C 571 " pdb=" C ASP C 571 " pdb=" CB ASP C 571 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CA ASP B1041 " pdb=" N ASP B1041 " pdb=" C ASP B1041 " pdb=" CB ASP B1041 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CA ASP C1041 " pdb=" N ASP C1041 " pdb=" C ASP C1041 " pdb=" CB ASP C1041 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.64e+00 ... (remaining 3530 not shown) Planarity restraints: 3876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 396 " -0.147 2.00e-02 2.50e+03 7.84e-02 1.23e+02 pdb=" CG TYR C 396 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR C 396 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TYR C 396 " 0.064 2.00e-02 2.50e+03 pdb=" CE1 TYR C 396 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR C 396 " 0.041 2.00e-02 2.50e+03 pdb=" CZ TYR C 396 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 396 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " 0.100 2.00e-02 2.50e+03 6.40e-02 1.02e+02 pdb=" CG TRP C 886 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.075 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " -0.048 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " -0.036 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.096 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.047 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 104 " 0.101 2.00e-02 2.50e+03 6.05e-02 9.15e+01 pdb=" CG TRP C 104 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP C 104 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP C 104 " -0.051 2.00e-02 2.50e+03 pdb=" NE1 TRP C 104 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP C 104 " -0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP C 104 " -0.099 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 104 " 0.062 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 104 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP C 104 " 0.080 2.00e-02 2.50e+03 ... (remaining 3873 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 11363 3.02 - 3.49: 20911 3.49 - 3.96: 34272 3.96 - 4.43: 38283 4.43 - 4.90: 64953 Nonbonded interactions: 169782 Sorted by model distance: nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.552 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.553 3.040 nonbonded pdb=" OD1 ASP A 294 " pdb=" OG SER A 297 " model vdw 2.555 3.040 nonbonded pdb=" OG SER A 94 " pdb=" OE2 GLU A 96 " model vdw 2.558 3.040 nonbonded pdb=" OD1 ASP B 294 " pdb=" OG SER B 297 " model vdw 2.571 3.040 ... (remaining 169777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 332 or (resid 333 through 334 and (name N or name CA or name C or name O or \ name CB )) or resid 335 through 345 or (resid 346 through 360 and (name N or na \ me CA or name C or name O or name CB )) or resid 361 or (resid 362 through 378 a \ nd (name N or name CA or name C or name O or name CB )) or resid 379 or (resid 3 \ 80 and (name N or name CA or name C or name O or name CB )) or resid 381 or (res \ id 382 through 383 and (name N or name CA or name C or name O or name CB )) or r \ esid 384 or (resid 385 through 390 and (name N or name CA or name C or name O or \ name CB )) or resid 391 or (resid 392 through 403 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 404 through 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 through 41 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 416 or (resi \ d 417 through 425 and (name N or name CA or name C or name O or name CB )) or re \ sid 426 through 427 or (resid 428 through 430 and (name N or name CA or name C o \ r name O or name CB )) or resid 431 through 432 or (resid 433 through 442 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 450 through 451 and \ (name N or name CA or name C or name O or name CB )) or (resid 453 and (name N \ or name CA or name C or name O or name CB )) or resid 463 or (resid 464 through \ 466 and (name N or name CA or name C or name O or name CB )) or resid 491 or (re \ sid 492 through 495 and (name N or name CA or name C or name O or name CB )) or \ resid 496 or (resid 497 through 498 and (name N or name CA or name C or name O o \ r name CB )) or resid 499 or (resid 500 through 503 and (name N or name CA or na \ me C or name O or name CB )) or (resid 504 through 506 and (name N or name CA or \ name C or name O or name CB )) or resid 507 or (resid 508 through 515 and (name \ N or name CA or name C or name O or name CB )) or (resid 522 through 524 and (n \ ame N or name CA or name C or name O or name CB )) or resid 525 through 528 or ( \ resid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 \ through 553 or (resid 554 and (name N or name CA or name C or name O or name CB \ )) or resid 555 through 793 or (resid 794 and (name N or name CA or name C or na \ me O or name CB )) or resid 795 or (resid 796 and (name N or name CA or name C o \ r name O or name CB )) or resid 797 through 810 or (resid 811 and (name N or nam \ e CA or name C or name O or name CB )) or resid 813 through 866 or (resid 867 th \ rough 868 and (name N or name CA or name C or name O or name CB )) or resid 869 \ through 939 or (resid 940 and (name N or name CA or name C or name O or name CB \ )) or resid 941 through 984 or (resid 985 and (name N or name CA or name C or na \ me O or name CB )) or resid 986 through 987 or (resid 988 through 989 and (name \ N or name CA or name C or name O or name CB )) or resid 990 through 1141 or (res \ id 1142 and (name N or name CA or name C or name O or name CB )) or resid 1143 t \ hrough 1144 or (resid 1145 through 1146 and (name N or name CA or name C or name \ O or name CB )) or resid 1147)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 442 or resid 450 through 451 or resid 453 or resid 46 \ 3 through 501 or resid 503 through 567 or (resid 568 and (name N or name CA or n \ ame C or name O or name CB )) or resid 569 through 570 or (resid 571 and (name N \ or name CA or name C or name O or name CB )) or resid 572 through 581 or (resid \ 582 through 583 and (name N or name CA or name C or name O or name CB )) or res \ id 584 through 585 or (resid 586 and (name N or name CA or name C or name O or n \ ame CB )) or resid 587 through 613 or (resid 614 and (name N or name CA or name \ C or name O or name CB )) or resid 615 through 618 or (resid 619 and (name N or \ name CA or name C or name O or name CB )) or resid 620 through 676 or resid 690 \ through 744 or (resid 745 and (name N or name CA or name C or name O or name CB \ )) or resid 746 through 810 or (resid 811 and (name N or name CA or name C or na \ me O or name CB )) or resid 813 through 866 or (resid 867 through 868 and (name \ N or name CA or name C or name O or name CB )) or resid 869 through 920 or (resi \ d 921 and (name N or name CA or name C or name O or name CB )) or resid 922 thro \ ugh 939 or (resid 940 and (name N or name CA or name C or name O or name CB )) o \ r resid 941 through 984 or (resid 985 and (name N or name CA or name C or name O \ or name CB )) or resid 986 through 987 or (resid 988 through 989 and (name N or \ name CA or name C or name O or name CB )) or resid 990 through 1072 or (resid 1 \ 073 and (name N or name CA or name C or name O or name CB )) or resid 1074 throu \ gh 1117 or (resid 1118 and (name N or name CA or name C or name O or name CB )) \ or resid 1119 through 1143 or (resid 1144 through 1146 and (name N or name CA or \ name C or name O or name CB )) or resid 1147)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 332 or (resid 333 thro \ ugh 334 and (name N or name CA or name C or name O or name CB )) or resid 335 th \ rough 344 or (resid 345 through 360 and (name N or name CA or name C or name O o \ r name CB )) or resid 361 or (resid 362 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 379 or (resid 380 and (name N or name CA o \ r name C or name O or name CB )) or resid 381 or (resid 382 through 383 and (nam \ e N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 thro \ ugh 390 and (name N or name CA or name C or name O or name CB )) or resid 391 or \ (resid 392 through 403 and (name N or name CA or name C or name O or name CB )) \ or (resid 404 through 411 and (name N or name CA or name C or name O or name CB \ )) or resid 412 through 413 or (resid 414 through 415 and (name N or name CA or \ name C or name O or name CB )) or (resid 416 through 425 and (name N or name CA \ or name C or name O or name CB )) or resid 426 or (resid 427 through 430 and (n \ ame N or name CA or name C or name O or name CB )) or resid 431 through 432 or ( \ resid 433 through 442 and (name N or name CA or name C or name O or name CB )) o \ r (resid 448 through 449 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 451 and (name N or name CA or name C or name O or name CB )) or resi \ d 463 or (resid 464 through 466 and (name N or name CA or name C or name O or na \ me CB )) or resid 491 or (resid 492 through 495 and (name N or name CA or name C \ or name O or name CB )) or resid 496 or (resid 497 through 498 and (name N or n \ ame CA or name C or name O or name CB )) or resid 499 through 500 or (resid 501 \ and (name N or name CA or name C or name O or name CB )) or (resid 503 and (name \ N or name CA or name C or name O or name CB )) or (resid 504 through 506 and (n \ ame N or name CA or name C or name O or name CB )) or resid 507 or (resid 508 th \ rough 515 and (name N or name CA or name C or name O or name CB )) or (resid 522 \ through 524 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 25 through 527 or (resid 528 through 529 and (name N or name CA or name C or nam \ e O or name CB )) or resid 530 through 553 or (resid 554 and (name N or name CA \ or name C or name O or name CB )) or resid 555 through 567 or (resid 568 and (na \ me N or name CA or name C or name O or name CB )) or resid 569 through 570 or (r \ esid 571 and (name N or name CA or name C or name O or name CB )) or resid 572 t \ hrough 581 or (resid 582 through 583 and (name N or name CA or name C or name O \ or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA or n \ ame C or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 620 through 645 or (resid \ 646 through 647 and (name N or name CA or name C or name O or name CB )) or res \ id 648 through 793 or (resid 794 and (name N or name CA or name C or name O or n \ ame CB )) or resid 795 or (resid 796 and (name N or name CA or name C or name O \ or name CB )) or resid 797 through 920 or (resid 921 and (name N or name CA or n \ ame C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and (name \ N or name CA or name C or name O or name CB )) or resid 1074 through 1117 or (r \ esid 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 \ through 1141 or (resid 1142 and (name N or name CA or name C or name O or name \ CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name CA or name C \ or name O or name CB )) or resid 1147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.870 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 : 0.012 0.044 22052 Z= 0.696 Angle : 1.756 8.246 30093 Z= 1.189 Chirality : 0.088 0.428 3533 Planarity : 0.012 0.141 3876 Dihedral : 12.508 89.738 7569 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.29 % Favored : 93.31 % Rotamer: Outliers : 1.64 % Allowed : 3.54 % Favored : 94.83 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.15), residues: 2797 helix: -0.98 (0.18), residues: 647 sheet: -0.14 (0.21), residues: 547 loop : -1.07 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 328 TYR 0.147 0.021 TYR C 396 PHE 0.077 0.012 PHE C 58 TRP 0.101 0.023 TRP C 104 HIS 0.014 0.003 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.01194 (22018) covalent geometry : angle 1.75619 (30025) SS BOND : bond 0.00759 ( 34) SS BOND : angle 1.81893 ( 68) hydrogen bonds : bond 0.16067 ( 972) hydrogen bonds : angle 8.67885 ( 2661) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8534 (p90) REVERT: A 378 LYS cc_start: 0.8246 (tttt) cc_final: 0.7960 (ttmm) REVERT: A 383 SER cc_start: 0.8401 (m) cc_final: 0.8191 (m) REVERT: B 1037 SER cc_start: 0.8706 (t) cc_final: 0.8419 (p) REVERT: C 84 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7315 (mp) REVERT: C 497 PHE cc_start: 0.4320 (m-80) cc_final: 0.3803 (m-80) outliers start: 37 outliers final: 15 residues processed: 203 average time/residue: 0.1658 time to fit residues: 52.2174 Evaluate side-chains 96 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.0470 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 506 GLN A1135 ASN B 343 ASN B 764 ASN B 784 GLN C 218 GLN C 580 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.092955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.069188 restraints weight = 51878.630| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.36 r_work: 0.2994 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22052 Z= 0.146 Angle : 0.610 9.850 30093 Z= 0.324 Chirality : 0.045 0.247 3533 Planarity : 0.004 0.035 3876 Dihedral : 6.077 57.601 3054 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.64 % Allowed : 6.01 % Favored : 92.35 % 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 are not related in a simple way. whole: -0.32 (0.15), residues: 2797 helix: 0.92 (0.20), residues: 657 sheet: -0.18 (0.19), residues: 650 loop : -0.70 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 214 TYR 0.016 0.002 TYR C1067 PHE 0.021 0.002 PHE B 135 TRP 0.010 0.001 TRP A 104 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00327 (22018) covalent geometry : angle 0.60666 (30025) SS BOND : bond 0.00383 ( 34) SS BOND : angle 1.50904 ( 68) hydrogen bonds : bond 0.04440 ( 972) hydrogen bonds : angle 6.21805 ( 2661) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6931 (OUTLIER) cc_final: 0.5050 (m100) REVERT: A 318 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7616 (p90) REVERT: A 856 ILE cc_start: 0.8939 (pp) cc_final: 0.8716 (pp) REVERT: A 869 MET cc_start: 0.9139 (mtp) cc_final: 0.8740 (mtp) REVERT: B 231 ILE cc_start: 0.9221 (pt) cc_final: 0.8987 (mm) REVERT: B 856 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8739 (tp) REVERT: B 979 ASP cc_start: 0.8862 (m-30) cc_final: 0.8595 (t70) REVERT: B 1002 GLN cc_start: 0.8588 (tt0) cc_final: 0.8016 (tp40) REVERT: C 84 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6945 (mp) REVERT: C 200 TYR cc_start: 0.8372 (m-80) cc_final: 0.8169 (m-80) REVERT: C 497 PHE cc_start: 0.3894 (m-10) cc_final: 0.3364 (m-80) REVERT: C 740 MET cc_start: 0.8944 (ttt) cc_final: 0.8742 (ttt) outliers start: 37 outliers final: 18 residues processed: 125 average time/residue: 0.1222 time to fit residues: 26.8443 Evaluate side-chains 95 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 108 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 78 optimal weight: 0.1980 chunk 223 optimal weight: 0.2980 chunk 142 optimal weight: 0.0010 chunk 63 optimal weight: 0.7980 chunk 55 optimal weight: 0.0030 chunk 252 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 261 optimal weight: 0.6980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 HIS B 907 ASN B 965 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.091984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.068180 restraints weight = 51798.756| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.39 r_work: 0.2998 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 22052 Z= 0.098 Angle : 0.519 9.932 30093 Z= 0.270 Chirality : 0.042 0.149 3533 Planarity : 0.004 0.035 3876 Dihedral : 5.184 59.329 3052 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.59 % Allowed : 7.03 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.16), residues: 2797 helix: 1.45 (0.20), residues: 673 sheet: -0.09 (0.20), residues: 626 loop : -0.55 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 214 TYR 0.017 0.001 TYR C1067 PHE 0.021 0.001 PHE B 135 TRP 0.009 0.001 TRP C 104 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00200 (22018) covalent geometry : angle 0.51713 (30025) SS BOND : bond 0.00319 ( 34) SS BOND : angle 0.98774 ( 68) hydrogen bonds : bond 0.03533 ( 972) hydrogen bonds : angle 5.54872 ( 2661) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.7717 (p90) REVERT: A 723 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8325 (p) REVERT: A 856 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8503 (pp) REVERT: A 869 MET cc_start: 0.9115 (mtp) cc_final: 0.8728 (mtp) REVERT: B 63 THR cc_start: 0.7429 (m) cc_final: 0.7054 (p) REVERT: B 229 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8273 (pp) REVERT: B 231 ILE cc_start: 0.9286 (pt) cc_final: 0.9059 (mm) REVERT: B 979 ASP cc_start: 0.8938 (m-30) cc_final: 0.8689 (t70) REVERT: B 1002 GLN cc_start: 0.8624 (tt0) cc_final: 0.8014 (tp40) REVERT: C 200 TYR cc_start: 0.8417 (m-80) cc_final: 0.8185 (m-80) REVERT: C 497 PHE cc_start: 0.3713 (m-10) cc_final: 0.3279 (m-80) REVERT: C 586 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: C 762 GLN cc_start: 0.9034 (pt0) cc_final: 0.8639 (tp40) REVERT: C 990 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8534 (tm-30) outliers start: 36 outliers final: 15 residues processed: 117 average time/residue: 0.1269 time to fit residues: 26.0097 Evaluate side-chains 95 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 856 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 163 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 130 optimal weight: 50.0000 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 259 optimal weight: 5.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.089372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.065266 restraints weight = 53903.211| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.23 r_work: 0.2980 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22052 Z= 0.166 Angle : 0.531 11.743 30093 Z= 0.274 Chirality : 0.043 0.154 3533 Planarity : 0.004 0.038 3876 Dihedral : 4.770 56.457 3039 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 2.17 % Allowed : 7.29 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.16), residues: 2797 helix: 1.64 (0.21), residues: 666 sheet: -0.10 (0.20), residues: 617 loop : -0.52 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.018 0.001 TYR A1067 PHE 0.019 0.002 PHE B 135 TRP 0.008 0.001 TRP A 104 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00388 (22018) covalent geometry : angle 0.52800 (30025) SS BOND : bond 0.00304 ( 34) SS BOND : angle 1.31521 ( 68) hydrogen bonds : bond 0.03550 ( 972) hydrogen bonds : angle 5.50077 ( 2661) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 76 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 723 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8540 (p) REVERT: A 856 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8505 (pp) REVERT: A 869 MET cc_start: 0.9175 (mtp) cc_final: 0.8867 (mtp) REVERT: A 873 TYR cc_start: 0.9134 (OUTLIER) cc_final: 0.8106 (m-10) REVERT: B 856 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8799 (tp) REVERT: B 979 ASP cc_start: 0.8941 (m-30) cc_final: 0.8730 (t70) REVERT: B 1002 GLN cc_start: 0.8742 (tt0) cc_final: 0.8286 (tp40) REVERT: C 200 TYR cc_start: 0.8475 (m-80) cc_final: 0.8239 (m-80) REVERT: C 497 PHE cc_start: 0.3481 (m-10) cc_final: 0.3045 (m-80) REVERT: C 586 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: C 762 GLN cc_start: 0.9027 (pt0) cc_final: 0.8593 (tp40) REVERT: C 990 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8519 (tm-30) outliers start: 49 outliers final: 30 residues processed: 113 average time/residue: 0.1221 time to fit residues: 24.6205 Evaluate side-chains 99 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 64 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 87 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 211 optimal weight: 0.5980 chunk 164 optimal weight: 0.3980 chunk 212 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.090849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.067000 restraints weight = 53386.796| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.22 r_work: 0.3017 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22052 Z= 0.100 Angle : 0.482 8.850 30093 Z= 0.249 Chirality : 0.042 0.152 3533 Planarity : 0.003 0.039 3876 Dihedral : 4.269 48.335 3035 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.75 % Rotamer: Outliers : 1.68 % Allowed : 8.05 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.16), residues: 2797 helix: 1.95 (0.21), residues: 665 sheet: -0.06 (0.20), residues: 617 loop : -0.45 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 34 TYR 0.016 0.001 TYR B1067 PHE 0.013 0.001 PHE C 400 TRP 0.008 0.001 TRP C 104 HIS 0.002 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00221 (22018) covalent geometry : angle 0.47998 (30025) SS BOND : bond 0.00235 ( 34) SS BOND : angle 1.05397 ( 68) hydrogen bonds : bond 0.03254 ( 972) hydrogen bonds : angle 5.25145 ( 2661) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 78 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 723 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8508 (p) REVERT: A 856 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8500 (pp) REVERT: A 869 MET cc_start: 0.9158 (mtp) cc_final: 0.8851 (mtp) REVERT: B 856 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8779 (tp) REVERT: B 979 ASP cc_start: 0.8925 (m-30) cc_final: 0.8721 (m-30) REVERT: B 1002 GLN cc_start: 0.8731 (tt0) cc_final: 0.8218 (tp40) REVERT: C 269 TYR cc_start: 0.8512 (m-80) cc_final: 0.8302 (m-80) REVERT: C 497 PHE cc_start: 0.3462 (m-10) cc_final: 0.3061 (m-80) REVERT: C 586 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7693 (t0) REVERT: C 762 GLN cc_start: 0.8957 (pt0) cc_final: 0.8554 (tp40) REVERT: C 990 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8469 (tm-30) outliers start: 38 outliers final: 25 residues processed: 107 average time/residue: 0.1236 time to fit residues: 23.1851 Evaluate side-chains 98 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 100 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 257 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.088765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.063975 restraints weight = 55392.274| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.34 r_work: 0.2947 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22052 Z= 0.222 Angle : 0.556 12.800 30093 Z= 0.284 Chirality : 0.044 0.164 3533 Planarity : 0.004 0.039 3876 Dihedral : 4.472 47.572 3035 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 2.21 % Allowed : 8.22 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.16), residues: 2797 helix: 1.69 (0.21), residues: 679 sheet: -0.25 (0.20), residues: 661 loop : -0.45 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.021 0.002 TYR A1067 PHE 0.019 0.002 PHE B1089 TRP 0.006 0.001 TRP A 104 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00518 (22018) covalent geometry : angle 0.55274 (30025) SS BOND : bond 0.00404 ( 34) SS BOND : angle 1.32760 ( 68) hydrogen bonds : bond 0.03617 ( 972) hydrogen bonds : angle 5.46869 ( 2661) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 69 time to evaluate : 0.802 Fit side-chains REVERT: A 378 LYS cc_start: 0.8016 (tttt) cc_final: 0.7612 (ttmm) REVERT: A 383 SER cc_start: 0.8808 (m) cc_final: 0.8457 (p) REVERT: A 417 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8579 (tppt) REVERT: A 723 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8598 (p) REVERT: A 856 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8527 (pp) REVERT: A 873 TYR cc_start: 0.9179 (OUTLIER) cc_final: 0.8308 (m-10) REVERT: B 856 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8775 (tp) REVERT: B 979 ASP cc_start: 0.8959 (m-30) cc_final: 0.8719 (t70) REVERT: B 1002 GLN cc_start: 0.8779 (tt0) cc_final: 0.8312 (tp40) REVERT: C 497 PHE cc_start: 0.3525 (m-10) cc_final: 0.3136 (m-80) REVERT: C 586 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7736 (t0) REVERT: C 762 GLN cc_start: 0.9065 (pt0) cc_final: 0.8706 (tp40) REVERT: C 990 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8504 (tm-30) outliers start: 50 outliers final: 32 residues processed: 108 average time/residue: 0.1313 time to fit residues: 24.6833 Evaluate side-chains 101 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 64 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 132 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 31 optimal weight: 0.0270 chunk 191 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 123 optimal weight: 40.0000 chunk 133 optimal weight: 30.0000 chunk 169 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.090276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.066415 restraints weight = 53626.813| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.23 r_work: 0.3003 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22052 Z= 0.102 Angle : 0.482 10.732 30093 Z= 0.248 Chirality : 0.042 0.162 3533 Planarity : 0.003 0.043 3876 Dihedral : 4.158 42.074 3035 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.82 % Rotamer: Outliers : 1.81 % Allowed : 8.89 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.16), residues: 2797 helix: 2.01 (0.21), residues: 669 sheet: -0.14 (0.20), residues: 641 loop : -0.38 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 273 TYR 0.016 0.001 TYR C1067 PHE 0.014 0.001 PHE B 135 TRP 0.009 0.001 TRP C 104 HIS 0.002 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00230 (22018) covalent geometry : angle 0.47947 (30025) SS BOND : bond 0.00305 ( 34) SS BOND : angle 1.04682 ( 68) hydrogen bonds : bond 0.03221 ( 972) hydrogen bonds : angle 5.21325 ( 2661) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 82 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8986 (mmmm) cc_final: 0.8648 (tppt) REVERT: A 723 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8582 (p) REVERT: A 856 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8555 (pp) REVERT: A 869 MET cc_start: 0.9127 (mtp) cc_final: 0.8825 (mtp) REVERT: A 873 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.8196 (m-10) REVERT: A 1141 LEU cc_start: 0.8830 (tp) cc_final: 0.8603 (tt) REVERT: B 534 VAL cc_start: 0.8952 (t) cc_final: 0.8596 (m) REVERT: B 856 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8792 (tp) REVERT: B 979 ASP cc_start: 0.8969 (m-30) cc_final: 0.8735 (t70) REVERT: B 1002 GLN cc_start: 0.8741 (tt0) cc_final: 0.8255 (tp40) REVERT: C 118 LEU cc_start: 0.8400 (tt) cc_final: 0.7844 (mp) REVERT: C 497 PHE cc_start: 0.3562 (m-10) cc_final: 0.3155 (m-80) REVERT: C 586 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7691 (t0) REVERT: C 762 GLN cc_start: 0.8994 (pt0) cc_final: 0.8587 (tp40) REVERT: C 990 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8492 (tm-30) outliers start: 41 outliers final: 28 residues processed: 112 average time/residue: 0.1276 time to fit residues: 25.0575 Evaluate side-chains 106 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 226 optimal weight: 20.0000 chunk 173 optimal weight: 0.0670 chunk 54 optimal weight: 6.9990 chunk 264 optimal weight: 6.9990 chunk 245 optimal weight: 0.0050 chunk 56 optimal weight: 5.9990 chunk 257 optimal weight: 6.9990 chunk 121 optimal weight: 40.0000 chunk 192 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.8138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.088856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.064565 restraints weight = 53078.485| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.46 r_work: 0.2925 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22052 Z= 0.166 Angle : 0.509 10.051 30093 Z= 0.260 Chirality : 0.042 0.147 3533 Planarity : 0.004 0.046 3876 Dihedral : 4.209 39.472 3035 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.64 % Rotamer: Outliers : 1.86 % Allowed : 9.02 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.16), residues: 2797 helix: 1.92 (0.21), residues: 676 sheet: -0.17 (0.20), residues: 645 loop : -0.43 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 273 TYR 0.019 0.001 TYR A1067 PHE 0.014 0.001 PHE A1121 TRP 0.006 0.001 TRP A 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00388 (22018) covalent geometry : angle 0.50684 (30025) SS BOND : bond 0.00268 ( 34) SS BOND : angle 1.16538 ( 68) hydrogen bonds : bond 0.03362 ( 972) hydrogen bonds : angle 5.25968 ( 2661) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 69 time to evaluate : 0.816 Fit side-chains REVERT: A 378 LYS cc_start: 0.7747 (tttt) cc_final: 0.7389 (ttmm) REVERT: A 417 LYS cc_start: 0.8924 (mmmm) cc_final: 0.8499 (tppt) REVERT: A 723 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8426 (p) REVERT: A 856 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8546 (pp) REVERT: A 869 MET cc_start: 0.9151 (mtp) cc_final: 0.8864 (mtp) REVERT: A 873 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.8221 (m-10) REVERT: A 1141 LEU cc_start: 0.8759 (tp) cc_final: 0.8538 (tt) REVERT: B 534 VAL cc_start: 0.8942 (t) cc_final: 0.8575 (m) REVERT: B 979 ASP cc_start: 0.8962 (m-30) cc_final: 0.8678 (t70) REVERT: B 1002 GLN cc_start: 0.8700 (tt0) cc_final: 0.8152 (tp40) REVERT: C 118 LEU cc_start: 0.8410 (tt) cc_final: 0.7837 (mp) REVERT: C 497 PHE cc_start: 0.3480 (m-10) cc_final: 0.3053 (m-80) REVERT: C 586 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7512 (t0) REVERT: C 762 GLN cc_start: 0.9053 (pt0) cc_final: 0.8590 (tp40) REVERT: C 990 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8500 (tm-30) outliers start: 42 outliers final: 32 residues processed: 101 average time/residue: 0.1232 time to fit residues: 21.9524 Evaluate side-chains 104 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 68 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 7 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 173 optimal weight: 0.5980 chunk 228 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 913 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.089407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.065715 restraints weight = 52271.692| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.33 r_work: 0.2953 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22052 Z= 0.126 Angle : 0.485 9.449 30093 Z= 0.249 Chirality : 0.042 0.146 3533 Planarity : 0.003 0.041 3876 Dihedral : 4.066 34.461 3035 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.82 % Rotamer: Outliers : 1.72 % Allowed : 9.33 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.16), residues: 2797 helix: 2.10 (0.21), residues: 669 sheet: -0.13 (0.20), residues: 623 loop : -0.40 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 273 TYR 0.017 0.001 TYR A1067 PHE 0.012 0.001 PHE B 135 TRP 0.010 0.001 TRP C 353 HIS 0.002 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00292 (22018) covalent geometry : angle 0.48071 (30025) SS BOND : bond 0.00236 ( 34) SS BOND : angle 1.37810 ( 68) hydrogen bonds : bond 0.03212 ( 972) hydrogen bonds : angle 5.15817 ( 2661) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 72 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8571 (tppt) REVERT: A 723 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8416 (p) REVERT: A 856 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8560 (pp) REVERT: A 869 MET cc_start: 0.9141 (mtp) cc_final: 0.8767 (mtp) REVERT: A 873 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.8132 (m-10) REVERT: A 1141 LEU cc_start: 0.8783 (tp) cc_final: 0.8555 (tt) REVERT: B 534 VAL cc_start: 0.8961 (t) cc_final: 0.8594 (m) REVERT: B 979 ASP cc_start: 0.8986 (m-30) cc_final: 0.8694 (t70) REVERT: B 1002 GLN cc_start: 0.8684 (tt0) cc_final: 0.8133 (tp40) REVERT: C 118 LEU cc_start: 0.8382 (tt) cc_final: 0.7829 (mp) REVERT: C 497 PHE cc_start: 0.3535 (m-10) cc_final: 0.3097 (m-80) REVERT: C 586 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7511 (t0) REVERT: C 762 GLN cc_start: 0.9004 (pt0) cc_final: 0.8562 (tp40) REVERT: C 990 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8470 (tm-30) outliers start: 39 outliers final: 29 residues processed: 102 average time/residue: 0.1221 time to fit residues: 22.2591 Evaluate side-chains 105 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 72 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 181 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 106 optimal weight: 0.0000 chunk 33 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 277 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 276 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.090570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.066860 restraints weight = 53709.489| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.26 r_work: 0.3019 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22052 Z= 0.095 Angle : 0.468 8.994 30093 Z= 0.241 Chirality : 0.041 0.146 3533 Planarity : 0.003 0.042 3876 Dihedral : 3.927 31.583 3035 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 1.50 % Allowed : 9.64 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.16), residues: 2797 helix: 2.14 (0.21), residues: 678 sheet: -0.08 (0.20), residues: 632 loop : -0.33 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 273 TYR 0.016 0.001 TYR B1067 PHE 0.016 0.001 PHE A 759 TRP 0.012 0.001 TRP C 353 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00209 (22018) covalent geometry : angle 0.46561 (30025) SS BOND : bond 0.00207 ( 34) SS BOND : angle 1.05934 ( 68) hydrogen bonds : bond 0.03084 ( 972) hydrogen bonds : angle 5.05523 ( 2661) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.9018 (mmmm) cc_final: 0.8723 (tppt) REVERT: A 723 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8612 (p) REVERT: A 856 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8578 (pp) REVERT: A 869 MET cc_start: 0.9097 (mtp) cc_final: 0.8799 (mtp) REVERT: A 873 TYR cc_start: 0.9136 (OUTLIER) cc_final: 0.8209 (m-10) REVERT: A 1141 LEU cc_start: 0.8869 (tp) cc_final: 0.8623 (tt) REVERT: B 63 THR cc_start: 0.7797 (m) cc_final: 0.7439 (p) REVERT: B 534 VAL cc_start: 0.8963 (t) cc_final: 0.8626 (m) REVERT: B 979 ASP cc_start: 0.8975 (m-30) cc_final: 0.8707 (t70) REVERT: B 1002 GLN cc_start: 0.8712 (tt0) cc_final: 0.8231 (tp40) REVERT: C 118 LEU cc_start: 0.8354 (tt) cc_final: 0.7840 (mp) REVERT: C 497 PHE cc_start: 0.3604 (m-10) cc_final: 0.3173 (m-80) REVERT: C 586 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7704 (t0) REVERT: C 762 GLN cc_start: 0.8918 (pt0) cc_final: 0.8557 (tp40) REVERT: C 990 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8470 (tm-30) outliers start: 34 outliers final: 27 residues processed: 108 average time/residue: 0.1222 time to fit residues: 23.7634 Evaluate side-chains 103 residues out of total 2526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 194 optimal weight: 10.0000 chunk 277 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B1048 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.087183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.063422 restraints weight = 52856.945| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.42 r_work: 0.2900 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22052 Z= 0.235 Angle : 0.554 9.056 30093 Z= 0.284 Chirality : 0.044 0.167 3533 Planarity : 0.004 0.041 3876 Dihedral : 4.236 37.446 3034 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.25 % Rotamer: Outliers : 1.77 % Allowed : 9.50 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.16), residues: 2797 helix: 1.93 (0.20), residues: 676 sheet: -0.27 (0.20), residues: 639 loop : -0.44 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.022 0.002 TYR A1067 PHE 0.020 0.002 PHE A1121 TRP 0.012 0.001 TRP C 353 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00549 (22018) covalent geometry : angle 0.55251 (30025) SS BOND : bond 0.00338 ( 34) SS BOND : angle 1.10663 ( 68) hydrogen bonds : bond 0.03548 ( 972) hydrogen bonds : angle 5.34098 ( 2661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4245.55 seconds wall clock time: 73 minutes 43.34 seconds (4423.34 seconds total)