Starting phenix.real_space_refine on Mon May 26 01:41:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yz5_39685/05_2025/8yz5_39685.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yz5_39685/05_2025/8yz5_39685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yz5_39685/05_2025/8yz5_39685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yz5_39685/05_2025/8yz5_39685.map" model { file = "/net/cci-nas-00/data/ceres_data/8yz5_39685/05_2025/8yz5_39685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yz5_39685/05_2025/8yz5_39685.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 122 5.16 5 C 17620 2.51 5 N 4635 2.21 5 O 5300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27677 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 8023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8023 Classifications: {'peptide': 1027} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 49, 'TRANS': 977} Chain breaks: 8 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 8138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8138 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 52, 'TRANS': 989} Chain breaks: 6 Chain: "D" Number of atoms: 8102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8102 Classifications: {'peptide': 1037} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 51, 'TRANS': 985} Chain breaks: 8 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 889 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 884 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 16.47, per 1000 atoms: 0.60 Number of scatterers: 27677 At special positions: 0 Unit cell: (162.68, 181.77, 150.23, 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 122 16.00 O 5300 8.00 N 4635 7.00 C 17620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " 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=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.05 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=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.02 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.04 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.02 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 86 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 86 " 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: 6.91 Conformation dependent library (CDL) restraints added in 3.6 seconds 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6616 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 47 sheets defined 20.3% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.719A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.659A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.072A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.593A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.576A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.594A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.796A pdb=" N ASP C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 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 968 removed outlier: 3.618A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.981A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1031 removed outlier: 4.355A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1120 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 4.239A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.100A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 438 through 443 removed outlier: 4.070A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.765A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.564A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.802A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.173A pdb=" N ILE A 923 " --> pdb=" O ASN A 919 " (cutoff:3.500A) 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 968 removed outlier: 3.780A pdb=" N ASN A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.157A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1031 removed outlier: 4.122A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.547A pdb=" N GLU D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 364 through 371 Processing helix chain 'D' and resid 385 through 390 removed outlier: 4.025A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 390 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 408 removed outlier: 3.599A pdb=" N VAL D 407 " --> pdb=" O ARG D 403 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG D 408 " --> pdb=" O GLY D 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 403 through 408' Processing helix chain 'D' and resid 417 through 422 removed outlier: 4.284A pdb=" N TYR D 421 " --> pdb=" O LYS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 506 Processing helix chain 'D' and resid 746 through 755 Processing helix chain 'D' and resid 758 through 781 Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 866 through 883 Processing helix chain 'D' and resid 897 through 908 removed outlier: 3.816A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 941 removed outlier: 4.309A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 968 removed outlier: 3.657A pdb=" N ALA D 958 " --> pdb=" O GLN D 954 " (cutoff:3.500A) Processing helix chain 'D' and resid 977 through 982 removed outlier: 4.388A pdb=" N LEU D 981 " --> pdb=" O LEU D 977 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER D 982 " --> pdb=" O ASN D 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 977 through 982' Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.714A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1120 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.609A pdb=" N THR G 87 " --> pdb=" O ALA G 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 81 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.503A pdb=" N ILE J 81 " --> pdb=" O PRO J 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 5.830A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.508A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.869A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.664A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 141 through 142 removed outlier: 6.427A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 312 through 319 removed outlier: 5.443A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 325 through 327 Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.058A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.663A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.679A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 3.822A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.085A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.111A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 141 through 143 removed outlier: 3.973A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.527A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.411A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'A' and resid 664 through 667 removed outlier: 5.883A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 712 through 727 removed outlier: 6.794A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AC7, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AC8, first strand: chain 'D' and resid 29 through 31 removed outlier: 8.891A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA D 93 " --> pdb=" O TYR D 266 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY D 268 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 190 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU D 224 " --> pdb=" O SER D 205 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 47 through 55 removed outlier: 4.111A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 83 through 84 removed outlier: 4.080A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 311 through 318 removed outlier: 3.592A pdb=" N GLY D 311 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR D 599 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS D 649 " --> pdb=" O TYR D 612 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 324 through 326 removed outlier: 6.872A pdb=" N GLU D 324 " --> pdb=" O ASN D 540 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASN D 542 " --> pdb=" O GLU D 324 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE D 326 " --> pdb=" O ASN D 542 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 587 " --> pdb=" O ASP D 574 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AD5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'D' and resid 664 through 667 removed outlier: 5.831A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 711 through 727 removed outlier: 6.516A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASN D 717 " --> pdb=" O ALA D1070 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA D1070 " --> pdb=" O ASN D 717 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS D1064 " --> pdb=" O THR D 723 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'D' and resid 1081 through 1082 removed outlier: 4.263A pdb=" N ILE D1081 " --> pdb=" O HIS D1088 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'G' and resid 57 through 59 removed outlier: 3.590A pdb=" N TYR G 58 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AE5, first strand: chain 'K' and resid 19 through 22 Processing sheet with id=AE6, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.738A pdb=" N ASN K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR K 49 " --> pdb=" O ASN K 53 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN K 87 " --> pdb=" O ASN K 34 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'I' and resid 57 through 59 removed outlier: 4.841A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.806A pdb=" N LEU J 11 " --> pdb=" O LYS J 101 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU J 103 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 19 through 23 Processing sheet with id=AF2, first strand: chain 'J' and resid 34 through 37 removed outlier: 5.969A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) 993 hydrogen bonds defined for protein. 2697 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: 11.76 Time building geometry restraints manager: 7.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8938 1.34 - 1.46: 6592 1.46 - 1.58: 12610 1.58 - 1.70: 1 1.70 - 1.83: 158 Bond restraints: 28299 Sorted by residual: bond pdb=" N ASN D 331 " pdb=" CA ASN D 331 " ideal model delta sigma weight residual 1.458 1.488 -0.029 1.14e-02 7.69e+03 6.56e+00 bond pdb=" N LEU D 335 " pdb=" CA LEU D 335 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.35e+00 bond pdb=" N ASN D 334 " pdb=" CA ASN D 334 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.30e-02 5.92e+03 5.26e+00 bond pdb=" N THR D 333 " pdb=" CA THR D 333 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.30e-02 5.92e+03 4.76e+00 bond pdb=" N ILE D 332 " pdb=" CA ILE D 332 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.25e-02 6.40e+03 4.40e+00 ... (remaining 28294 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 37991 2.44 - 4.87: 449 4.87 - 7.31: 37 7.31 - 9.75: 11 9.75 - 12.18: 1 Bond angle restraints: 38489 Sorted by residual: angle pdb=" N GLN A 954 " pdb=" CA GLN A 954 " pdb=" CB GLN A 954 " ideal model delta sigma weight residual 110.12 116.65 -6.53 1.47e+00 4.63e-01 1.98e+01 angle pdb=" C ASN C 953 " pdb=" N GLN C 954 " pdb=" CA GLN C 954 " ideal model delta sigma weight residual 121.18 113.02 8.16 1.98e+00 2.55e-01 1.70e+01 angle pdb=" C TYR K 49 " pdb=" N ASP K 50 " pdb=" CA ASP K 50 " ideal model delta sigma weight residual 121.54 129.13 -7.59 1.91e+00 2.74e-01 1.58e+01 angle pdb=" CA ARG C 765 " pdb=" CB ARG C 765 " pdb=" CG ARG C 765 " ideal model delta sigma weight residual 114.10 121.91 -7.81 2.00e+00 2.50e-01 1.53e+01 angle pdb=" CA PRO D1057 " pdb=" N PRO D1057 " pdb=" CD PRO D1057 " ideal model delta sigma weight residual 112.00 106.90 5.10 1.40e+00 5.10e-01 1.32e+01 ... (remaining 38484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 15486 17.86 - 35.71: 1092 35.71 - 53.57: 178 53.57 - 71.42: 46 71.42 - 89.28: 26 Dihedral angle restraints: 16828 sinusoidal: 6526 harmonic: 10302 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -161.26 75.26 1 1.00e+01 1.00e-02 7.16e+01 dihedral pdb=" CB CYS D 662 " pdb=" SG CYS D 662 " pdb=" SG CYS D 671 " pdb=" CB CYS D 671 " ideal model delta sinusoidal sigma weight residual 93.00 162.68 -69.68 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -19.72 -66.28 1 1.00e+01 1.00e-02 5.74e+01 ... (remaining 16825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3090 0.044 - 0.088: 889 0.088 - 0.132: 325 0.132 - 0.177: 42 0.177 - 0.221: 7 Chirality restraints: 4353 Sorted by residual: chirality pdb=" CG LEU D 948 " pdb=" CB LEU D 948 " pdb=" CD1 LEU D 948 " pdb=" CD2 LEU D 948 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CG LEU I 78 " pdb=" CB LEU I 78 " pdb=" CD1 LEU I 78 " pdb=" CD2 LEU I 78 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLN D 957 " pdb=" N GLN D 957 " pdb=" C GLN D 957 " pdb=" CB GLN D 957 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 4350 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D1056 " -0.074 5.00e-02 4.00e+02 1.09e-01 1.92e+01 pdb=" N PRO D1057 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO D1057 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO D1057 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 560 " 0.059 5.00e-02 4.00e+02 8.99e-02 1.29e+01 pdb=" N PRO C 561 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO C 561 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 561 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 896 " 0.050 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO D 897 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 897 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 897 " 0.042 5.00e-02 4.00e+02 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 7 2.16 - 2.85: 9516 2.85 - 3.53: 37429 3.53 - 4.22: 63012 4.22 - 4.90: 106716 Nonbonded interactions: 216680 Sorted by model distance: nonbonded pdb=" OD2 ASP D 142 " pdb=" CZ3 TRP D 258 " model vdw 1.479 3.340 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.053 3.040 nonbonded pdb=" OE2 GLU D 725 " pdb=" NZ LYS D1028 " model vdw 2.094 3.120 nonbonded pdb=" O VAL A 951 " pdb=" ND2 ASN A 955 " model vdw 2.101 3.120 nonbonded pdb=" OD2 ASP A 142 " pdb=" CZ2 TRP A 258 " model vdw 2.120 3.340 ... (remaining 216675 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 20 through 143 or resid 161 or resid 166 through 332 or re \ sid 335 through 356 or (resid 357 and (name N or name CA or name C or name O or \ name CB )) or resid 358 through 377 or (resid 378 and (name N or name CA or name \ C or name O or name CB )) or resid 379 through 390 or (resid 391 and (name N or \ name CA or name C or name O or name CB )) or resid 392 through 518 or resid 530 \ through 579 or (resid 580 and (name N or name CA or name C or name O or name CB \ )) or resid 581 through 1141)) selection = (chain 'C' and (resid 20 through 143 or resid 161 or resid 166 through 1141)) selection = (chain 'D' and (resid 20 through 143 or resid 151 or resid 166 through 332 or re \ sid 335 through 518 or resid 530 through 579 or (resid 580 and (name N or name C \ A or name C or name O or name CB )) or resid 581 through 1141)) } ncs_group { reference = (chain 'G' and resid 1 through 113) selection = chain 'I' } ncs_group { reference = (chain 'J' and resid 1 through 104) selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.210 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 63.180 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5060 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 : 0.003 0.070 28340 Z= 0.150 Angle : 0.664 12.182 38571 Z= 0.357 Chirality : 0.047 0.221 4353 Planarity : 0.005 0.109 4992 Dihedral : 12.984 89.276 10089 Min Nonbonded Distance : 1.479 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.95 % Favored : 93.97 % Rotamer: Outliers : 0.07 % Allowed : 0.29 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.14), residues: 3498 helix: -0.58 (0.21), residues: 592 sheet: -0.45 (0.19), residues: 750 loop : -1.66 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 64 HIS 0.011 0.001 HIS D1101 PHE 0.032 0.002 PHE C 275 TYR 0.029 0.002 TYR A 873 ARG 0.016 0.001 ARG C 577 Details of bonding type rmsd hydrogen bonds : bond 0.15089 ( 993) hydrogen bonds : angle 7.52657 ( 2697) SS BOND : bond 0.00426 ( 41) SS BOND : angle 1.66222 ( 82) covalent geometry : bond 0.00312 (28299) covalent geometry : angle 0.66057 (38489) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 374 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 658 ASN cc_start: 0.5996 (p0) cc_final: 0.5754 (p0) REVERT: A 43 PHE cc_start: 0.7469 (m-10) cc_final: 0.7150 (m-80) REVERT: A 815 ARG cc_start: 0.5600 (ptt-90) cc_final: 0.4166 (mtm110) REVERT: D 237 ARG cc_start: 0.4408 (ppt170) cc_final: 0.4110 (tmm160) REVERT: D 754 LEU cc_start: 0.6408 (mm) cc_final: 0.6096 (mt) REVERT: D 1107 ARG cc_start: 0.4523 (mtm180) cc_final: 0.3888 (tpt90) outliers start: 2 outliers final: 0 residues processed: 376 average time/residue: 0.3944 time to fit residues: 235.4187 Evaluate side-chains 294 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.5862 > 50: distance: 35 - 39: 35.925 distance: 39 - 40: 39.993 distance: 40 - 41: 57.175 distance: 40 - 43: 23.152 distance: 41 - 42: 55.743 distance: 43 - 44: 24.364 distance: 45 - 46: 56.273 distance: 46 - 47: 40.017 distance: 48 - 49: 41.068 distance: 49 - 50: 40.409 distance: 49 - 52: 55.842 distance: 50 - 51: 39.476 distance: 50 - 55: 40.568 distance: 52 - 53: 41.033 distance: 52 - 54: 57.825 distance: 55 - 56: 55.708 distance: 56 - 57: 56.462 distance: 57 - 58: 56.464 distance: 57 - 59: 40.892 distance: 59 - 60: 39.318 distance: 60 - 61: 40.181 distance: 61 - 63: 40.037 distance: 64 - 65: 56.221 distance: 64 - 67: 40.624 distance: 65 - 71: 70.078 distance: 68 - 69: 56.947 distance: 68 - 70: 68.795 distance: 72 - 73: 55.987 distance: 73 - 83: 58.631 distance: 75 - 76: 40.594 distance: 76 - 78: 8.915 distance: 77 - 79: 17.057 distance: 78 - 80: 41.479 distance: 79 - 81: 29.387 distance: 80 - 81: 17.521 distance: 81 - 82: 45.705 distance: 83 - 84: 28.066 distance: 84 - 85: 11.065 distance: 85 - 86: 42.670 distance: 85 - 91: 29.564 distance: 88 - 89: 69.555 distance: 92 - 93: 56.546 distance: 92 - 95: 55.809 distance: 95 - 96: 41.348 distance: 96 - 97: 57.072 distance: 96 - 98: 39.933 distance: 99 - 101: 57.144 distance: 100 - 101: 39.731 distance: 101 - 102: 69.696 distance: 103 - 104: 40.945 distance: 104 - 105: 38.717 distance: 104 - 107: 56.104 distance: 105 - 114: 57.035 distance: 108 - 109: 39.443 distance: 109 - 110: 57.826 distance: 110 - 111: 69.584 distance: 111 - 112: 55.509 distance: 111 - 113: 57.768 distance: 114 - 115: 38.780 distance: 114 - 150: 37.511 distance: 116 - 126: 35.061 distance: 117 - 147: 35.831 distance: 120 - 122: 70.406 distance: 121 - 123: 40.090 distance: 122 - 124: 40.318 distance: 123 - 124: 40.401 distance: 124 - 125: 57.051