Starting phenix.real_space_refine on Sun Jun 29 01:04:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e9q_31036/06_2025/7e9q_31036.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e9q_31036/06_2025/7e9q_31036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e9q_31036/06_2025/7e9q_31036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e9q_31036/06_2025/7e9q_31036.map" model { file = "/net/cci-nas-00/data/ceres_data/7e9q_31036/06_2025/7e9q_31036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e9q_31036/06_2025/7e9q_31036.cif" } resolution = 3.65 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= 1.000 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 147 5.16 5 C 21504 2.51 5 N 5622 2.21 5 O 6603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 176 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33876 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "A" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "C" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "L" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "X" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "Y" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "E" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "F" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 20.43, per 1000 atoms: 0.60 Number of scatterers: 33876 At special positions: 0 Unit cell: (191.625, 205.86, 227.76, 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 147 16.00 O 6603 8.00 N 5622 7.00 C 21504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.01 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 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=2.04 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=2.05 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=2.06 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 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=2.04 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 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 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 L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 157 " - pdb=" SG CYS H 213 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 93 " distance=2.03 Simple disulfide: pdb=" SG CYS X 139 " - pdb=" SG CYS X 199 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 157 " - pdb=" SG CYS Y 213 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.05 Simple disulfide: pdb=" SG CYS E 139 " - pdb=" SG CYS E 199 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 213 " distance=2.04 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A1098 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B1098 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " Time building additional restraints: 9.96 Conformation dependent library (CDL) restraints added in 7.1 seconds 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 65 sheets defined 18.4% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.89 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.752A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.584A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.839A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.731A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.587A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.536A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 7.031A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.933A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.757A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.074A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.967A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.079A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.540A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 967 removed outlier: 4.056A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.085A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.859A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 4.159A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.255A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.941A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.573A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 removed outlier: 3.641A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.663A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.613A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.617A pdb=" N ASP C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.503A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.557A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) 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 967 removed outlier: 3.839A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.718A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.757A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.556A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.867A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'L' and resid 188 through 194 removed outlier: 4.406A pdb=" N GLU L 192 " --> pdb=" O LYS L 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 173 through 175 No H-bonds generated for 'chain 'H' and resid 173 through 175' Processing helix chain 'H' and resid 204 through 206 No H-bonds generated for 'chain 'H' and resid 204 through 206' Processing helix chain 'X' and resid 84 through 88 Processing helix chain 'X' and resid 126 through 132 Processing helix chain 'Y' and resid 87 through 91 removed outlier: 3.982A pdb=" N THR Y 91 " --> pdb=" O ALA Y 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 192 removed outlier: 4.122A pdb=" N GLU E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.524A pdb=" N ASP F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.667A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.415A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.065A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.708A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.488A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 327 through 328 removed outlier: 3.708A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AA9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.888A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.614A pdb=" N ILE B 712 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AB3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AB4, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.520A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.952A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AB7, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AB8, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.703A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.296A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AC4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.925A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC6, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AC7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC8, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.701A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.175A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.504A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.834A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.252A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.548A pdb=" N ALA C 694 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.713A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.713A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AE2, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AE3, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AE4, first strand: chain 'L' and resid 58 through 59 removed outlier: 4.944A pdb=" N SER L 48 " --> pdb=" O LYS L 44 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS L 44 " --> pdb=" O SER L 48 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TYR L 54 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU L 38 " --> pdb=" O TYR L 54 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.925A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 158 through 160 removed outlier: 4.017A pdb=" N TRP L 153 " --> pdb=" O GLN L 160 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AE9, first strand: chain 'H' and resid 57 through 60 removed outlier: 7.002A pdb=" N GLY H 50 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR H 60 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL H 48 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 137 through 141 removed outlier: 6.393A pdb=" N TYR H 193 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 137 through 141 removed outlier: 6.393A pdb=" N TYR H 193 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 168 through 171 Processing sheet with id=AF4, first strand: chain 'X' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'X' and resid 50 through 54 removed outlier: 6.357A pdb=" N TRP X 40 " --> pdb=" O LEU X 52 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N TYR X 54 " --> pdb=" O LEU X 38 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU X 38 " --> pdb=" O TYR X 54 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 119 through 123 removed outlier: 5.408A pdb=" N SER X 136 " --> pdb=" O LEU X 186 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU X 186 " --> pdb=" O SER X 136 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL X 138 " --> pdb=" O LEU X 184 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU X 184 " --> pdb=" O VAL X 138 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU X 140 " --> pdb=" O SER X 182 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SER X 182 " --> pdb=" O LEU X 140 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASN X 142 " --> pdb=" O LEU X 180 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU X 180 " --> pdb=" O ASN X 142 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER X 179 " --> pdb=" O GLU X 170 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU X 170 " --> pdb=" O SER X 179 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER X 181 " --> pdb=" O VAL X 168 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL X 168 " --> pdb=" O SER X 181 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR X 183 " --> pdb=" O GLU X 166 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLU X 166 " --> pdb=" O THR X 183 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'X' and resid 159 through 160 removed outlier: 4.521A pdb=" N TRP X 153 " --> pdb=" O GLN X 160 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'Y' and resid 45 through 51 removed outlier: 6.758A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLY Y 50 " --> pdb=" O MET Y 34 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N MET Y 34 " --> pdb=" O GLY Y 50 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Y' and resid 137 through 141 removed outlier: 6.512A pdb=" N TYR Y 193 " --> pdb=" O ASP Y 161 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Y' and resid 137 through 141 removed outlier: 6.512A pdb=" N TYR Y 193 " --> pdb=" O ASP Y 161 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Y' and resid 167 through 171 removed outlier: 4.336A pdb=" N TYR Y 211 " --> pdb=" O VAL Y 228 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 19 through 21 Processing sheet with id=AG5, first strand: chain 'E' and resid 58 through 59 removed outlier: 6.456A pdb=" N TRP E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 119 through 123 removed outlier: 3.710A pdb=" N VAL E 138 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR E 178 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 150 through 154 removed outlier: 4.018A pdb=" N LYS E 150 " --> pdb=" O THR E 202 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AG9, first strand: chain 'F' and resid 45 through 51 removed outlier: 6.445A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS F 98 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL F 119 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.850A pdb=" N SER F 137 " --> pdb=" O LYS F 160 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N CYS F 157 " --> pdb=" O SER F 197 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER F 197 " --> pdb=" O CYS F 157 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER F 196 " --> pdb=" O PHE F 183 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 168 through 170 1314 hydrogen bonds defined for protein. 3495 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: 29.19 Time building geometry restraints manager: 11.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5562 1.30 - 1.43: 9381 1.43 - 1.57: 19509 1.57 - 1.70: 0 1.70 - 1.83: 189 Bond restraints: 34641 Sorted by residual: bond pdb=" CA SER A 816 " pdb=" CB SER A 816 " ideal model delta sigma weight residual 1.538 1.463 0.075 1.29e-02 6.01e+03 3.36e+01 bond pdb=" C PRO A 897 " pdb=" O PRO A 897 " ideal model delta sigma weight residual 1.233 1.166 0.067 1.16e-02 7.43e+03 3.30e+01 bond pdb=" C7 NAG A1305 " pdb=" N2 NAG A1305 " ideal model delta sigma weight residual 1.346 1.461 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C7 NAG C1304 " pdb=" N2 NAG C1304 " ideal model delta sigma weight residual 1.346 1.457 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C7 NAG A1304 " pdb=" N2 NAG A1304 " ideal model delta sigma weight residual 1.346 1.456 -0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 34636 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 45404 2.29 - 4.57: 1474 4.57 - 6.86: 235 6.86 - 9.15: 32 9.15 - 11.43: 3 Bond angle restraints: 47148 Sorted by residual: angle pdb=" N ILE X 111 " pdb=" CA ILE X 111 " pdb=" C ILE X 111 " ideal model delta sigma weight residual 110.72 119.54 -8.82 1.01e+00 9.80e-01 7.63e+01 angle pdb=" CA PRO A 897 " pdb=" C PRO A 897 " pdb=" O PRO A 897 " ideal model delta sigma weight residual 121.34 112.69 8.65 1.14e+00 7.69e-01 5.76e+01 angle pdb=" CA PRO A 897 " pdb=" C PRO A 897 " pdb=" N PHE A 898 " ideal model delta sigma weight residual 115.56 124.99 -9.43 1.27e+00 6.20e-01 5.51e+01 angle pdb=" CA PHE A 888 " pdb=" CB PHE A 888 " pdb=" CG PHE A 888 " ideal model delta sigma weight residual 113.80 120.51 -6.71 1.00e+00 1.00e+00 4.50e+01 angle pdb=" N PRO A 897 " pdb=" CA PRO A 897 " pdb=" CB PRO A 897 " ideal model delta sigma weight residual 103.31 97.35 5.96 8.90e-01 1.26e+00 4.48e+01 ... (remaining 47143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 19729 24.08 - 48.16: 961 48.16 - 72.24: 160 72.24 - 96.32: 70 96.32 - 120.40: 107 Dihedral angle restraints: 21027 sinusoidal: 8475 harmonic: 12552 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 177.80 -84.80 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -1.99 -84.01 1 1.00e+01 1.00e-02 8.60e+01 dihedral pdb=" CB CYS H 157 " pdb=" SG CYS H 157 " pdb=" SG CYS H 213 " pdb=" CB CYS H 213 " ideal model delta sinusoidal sigma weight residual 93.00 176.33 -83.33 1 1.00e+01 1.00e-02 8.48e+01 ... (remaining 21024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 4891 0.091 - 0.181: 486 0.181 - 0.272: 40 0.272 - 0.362: 13 0.362 - 0.453: 3 Chirality restraints: 5433 Sorted by residual: chirality pdb=" CB VAL B 524 " pdb=" CA VAL B 524 " pdb=" CG1 VAL B 524 " pdb=" CG2 VAL B 524 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA PHE C 338 " pdb=" N PHE C 338 " pdb=" C PHE C 338 " pdb=" CB PHE C 338 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 5430 not shown) Planarity restraints: 6099 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 938 " 0.021 2.00e-02 2.50e+03 4.14e-02 1.72e+01 pdb=" C LEU B 938 " -0.072 2.00e-02 2.50e+03 pdb=" O LEU B 938 " 0.027 2.00e-02 2.50e+03 pdb=" N SER B 939 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 887 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C THR B 887 " -0.067 2.00e-02 2.50e+03 pdb=" O THR B 887 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE B 888 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 84 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C GLU E 84 " -0.055 2.00e-02 2.50e+03 pdb=" O GLU E 84 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA E 85 " 0.018 2.00e-02 2.50e+03 ... (remaining 6096 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3535 2.75 - 3.29: 34221 3.29 - 3.82: 54454 3.82 - 4.36: 63463 4.36 - 4.90: 108003 Nonbonded interactions: 263676 Sorted by model distance: nonbonded pdb=" OH TYR A 369 " pdb=" O PRO A 384 " model vdw 2.209 3.040 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.210 3.040 nonbonded pdb=" OG SER X 70 " pdb=" OG1 THR X 77 " model vdw 2.210 3.040 nonbonded pdb=" OG SER C 359 " pdb=" OD1 ASN C 394 " model vdw 2.222 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.222 3.040 ... (remaining 263671 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'X' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'Y' } 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: 146.270 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: 0.030 Extract box with map and model: 1.430 Check model and map are aligned: 0.230 Set scattering table: 0.340 Process input model: 101.610 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.490 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: 0.050 Load rotamer database and sin/cos tables:4.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 256.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 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 : 0.007 0.115 34717 Z= 0.410 Angle : 0.939 11.431 47327 Z= 0.560 Chirality : 0.057 0.453 5433 Planarity : 0.006 0.068 6072 Dihedral : 17.925 120.402 12816 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.27 % Allowed : 1.36 % Favored : 98.38 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.12), residues: 4266 helix: 0.11 (0.20), residues: 668 sheet: -1.24 (0.14), residues: 1198 loop : -2.39 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP Y 36 HIS 0.007 0.001 HIS B1048 PHE 0.038 0.002 PHE A 888 TYR 0.025 0.002 TYR C 674 ARG 0.010 0.001 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 27) link_NAG-ASN : angle 2.24616 ( 81) hydrogen bonds : bond 0.13888 ( 1273) hydrogen bonds : angle 7.70122 ( 3495) SS BOND : bond 0.00854 ( 49) SS BOND : angle 2.27835 ( 98) covalent geometry : bond 0.00717 (34641) covalent geometry : angle 0.92990 (47148) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 323 time to evaluate : 3.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ILE cc_start: 0.7267 (mp) cc_final: 0.6012 (mm) REVERT: C 338 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7716 (t80) REVERT: H 134 LYS cc_start: 0.3647 (ttpp) cc_final: 0.3101 (mttt) REVERT: H 160 LYS cc_start: 0.2854 (mttm) cc_final: 0.1804 (pttm) REVERT: H 212 ILE cc_start: 0.1480 (OUTLIER) cc_final: 0.0726 (mt) REVERT: E 174 LYS cc_start: 0.3081 (mttt) cc_final: 0.2149 (pttt) REVERT: F 43 LYS cc_start: 0.3421 (mmtm) cc_final: 0.2126 (tmtt) outliers start: 10 outliers final: 1 residues processed: 332 average time/residue: 0.4982 time to fit residues: 264.4597 Evaluate side-chains 195 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 192 time to evaluate : 4.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain H residue 212 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 6.9990 chunk 325 optimal weight: 50.0000 chunk 180 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 219 optimal weight: 0.9980 chunk 173 optimal weight: 0.5980 chunk 336 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 204 optimal weight: 8.9990 chunk 250 optimal weight: 2.9990 chunk 389 optimal weight: 20.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 935 GLN B1005 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN C 804 GLN L 142 ASN X 165 GLN Y 1 GLN Y 181 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.189017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.159550 restraints weight = 66320.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.154931 restraints weight = 106440.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.152146 restraints weight = 92111.288| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 34717 Z= 0.192 Angle : 0.741 9.791 47327 Z= 0.373 Chirality : 0.051 0.351 5433 Planarity : 0.005 0.059 6072 Dihedral : 14.265 110.951 5201 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.01 % Allowed : 8.57 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.12), residues: 4266 helix: 0.76 (0.20), residues: 662 sheet: -1.03 (0.14), residues: 1194 loop : -2.32 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Y 47 HIS 0.006 0.001 HIS C1048 PHE 0.026 0.002 PHE X 144 TYR 0.026 0.002 TYR C1067 ARG 0.009 0.001 ARG Y 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 27) link_NAG-ASN : angle 2.57143 ( 81) hydrogen bonds : bond 0.05605 ( 1273) hydrogen bonds : angle 6.50699 ( 3495) SS BOND : bond 0.00407 ( 49) SS BOND : angle 1.74382 ( 98) covalent geometry : bond 0.00463 (34641) covalent geometry : angle 0.73041 (47148) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 4.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 660 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.7335 (m-80) REVERT: A 358 ILE cc_start: 0.7242 (mp) cc_final: 0.6735 (mm) REVERT: A 902 MET cc_start: 0.8594 (tpt) cc_final: 0.8340 (tpt) REVERT: H 84 ARG cc_start: 0.4153 (ptt90) cc_final: 0.3677 (ptt90) REVERT: H 134 LYS cc_start: 0.3357 (ttpp) cc_final: 0.3042 (mttt) REVERT: H 160 LYS cc_start: 0.2816 (mttm) cc_final: 0.1697 (pttm) REVERT: E 174 LYS cc_start: 0.3219 (mttt) cc_final: 0.2387 (pttt) REVERT: F 43 LYS cc_start: 0.3404 (mmtm) cc_final: 0.2090 (tmtt) outliers start: 38 outliers final: 22 residues processed: 246 average time/residue: 0.5397 time to fit residues: 216.7408 Evaluate side-chains 199 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 3.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 201 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 42 optimal weight: 30.0000 chunk 271 optimal weight: 1.9990 chunk 353 optimal weight: 40.0000 chunk 243 optimal weight: 20.0000 chunk 170 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.188289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.159517 restraints weight = 65761.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.153963 restraints weight = 103537.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.151379 restraints weight = 85797.431| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34717 Z= 0.128 Angle : 0.654 10.398 47327 Z= 0.327 Chirality : 0.047 0.325 5433 Planarity : 0.005 0.057 6072 Dihedral : 10.474 106.018 5198 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.68 % Allowed : 11.21 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -1.81 (0.13), residues: 4266 helix: 1.22 (0.20), residues: 664 sheet: -0.88 (0.14), residues: 1234 loop : -2.17 (0.12), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP Y 47 HIS 0.007 0.001 HIS C1048 PHE 0.030 0.001 PHE H 163 TYR 0.021 0.001 TYR C1067 ARG 0.007 0.001 ARG X 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 27) link_NAG-ASN : angle 2.29398 ( 81) hydrogen bonds : bond 0.04663 ( 1273) hydrogen bonds : angle 6.03248 ( 3495) SS BOND : bond 0.00338 ( 49) SS BOND : angle 1.50472 ( 98) covalent geometry : bond 0.00288 (34641) covalent geometry : angle 0.64430 (47148) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 222 time to evaluate : 3.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 ASN cc_start: 0.6439 (m-40) cc_final: 0.6051 (t0) REVERT: B 1107 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7616 (mtt180) REVERT: A 697 MET cc_start: 0.7415 (mtp) cc_final: 0.7123 (ttm) REVERT: A 902 MET cc_start: 0.8738 (tpt) cc_final: 0.8525 (tpt) REVERT: C 954 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7255 (mt0) REVERT: H 102 MET cc_start: 0.4482 (pmm) cc_final: 0.4061 (pmm) REVERT: H 134 LYS cc_start: 0.3044 (ttpp) cc_final: 0.2567 (ptpt) REVERT: H 160 LYS cc_start: 0.2832 (mttm) cc_final: 0.1765 (pttm) REVERT: E 4 MET cc_start: 0.2838 (tpp) cc_final: 0.2625 (tpp) REVERT: E 35 TYR cc_start: 0.1671 (OUTLIER) cc_final: 0.1004 (t80) REVERT: F 43 LYS cc_start: 0.3472 (mmtm) cc_final: 0.2134 (tmtt) outliers start: 63 outliers final: 34 residues processed: 272 average time/residue: 0.4528 time to fit residues: 205.5431 Evaluate side-chains 226 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain X residue 111 ILE Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain F residue 47 TRP Chi-restraints excluded: chain F residue 201 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 375 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 238 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 270 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 294 optimal weight: 4.9990 chunk 7 optimal weight: 0.3980 chunk 177 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 644 GLN C 218 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 HIS X 129 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.191944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.163957 restraints weight = 66983.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.159214 restraints weight = 100255.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.154307 restraints weight = 85636.724| |-----------------------------------------------------------------------------| r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 34717 Z= 0.154 Angle : 0.653 10.527 47327 Z= 0.327 Chirality : 0.047 0.257 5433 Planarity : 0.005 0.059 6072 Dihedral : 8.984 102.581 5198 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.48 % Allowed : 12.73 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.76 (0.12), residues: 4266 helix: 1.19 (0.20), residues: 662 sheet: -0.81 (0.14), residues: 1225 loop : -2.14 (0.12), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Y 47 HIS 0.004 0.001 HIS B1048 PHE 0.032 0.002 PHE B 135 TYR 0.021 0.001 TYR C1067 ARG 0.009 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 27) link_NAG-ASN : angle 2.47360 ( 81) hydrogen bonds : bond 0.04813 ( 1273) hydrogen bonds : angle 5.92329 ( 3495) SS BOND : bond 0.00482 ( 49) SS BOND : angle 1.70019 ( 98) covalent geometry : bond 0.00368 (34641) covalent geometry : angle 0.64175 (47148) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 208 time to evaluate : 3.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 ASP cc_start: 0.5433 (p0) cc_final: 0.5029 (p0) REVERT: B 317 ASN cc_start: 0.7870 (p0) cc_final: 0.7509 (p0) REVERT: B 343 ASN cc_start: 0.6542 (m-40) cc_final: 0.6005 (t0) REVERT: B 660 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.7342 (m-80) REVERT: B 977 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7713 (pp) REVERT: A 697 MET cc_start: 0.7341 (mtp) cc_final: 0.7122 (ttm) REVERT: C 945 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8411 (pp) REVERT: H 102 MET cc_start: 0.4382 (pmm) cc_final: 0.3885 (pmm) REVERT: H 134 LYS cc_start: 0.3227 (ttpp) cc_final: 0.2498 (ptpt) REVERT: H 160 LYS cc_start: 0.2487 (mttm) cc_final: 0.1486 (pttm) REVERT: Y 101 GLU cc_start: 0.5354 (OUTLIER) cc_final: 0.4274 (mp0) REVERT: E 35 TYR cc_start: 0.1869 (OUTLIER) cc_final: 0.1196 (t80) REVERT: E 174 LYS cc_start: 0.3219 (mttt) cc_final: 0.2277 (pttt) REVERT: F 43 LYS cc_start: 0.3398 (mmtm) cc_final: 0.2167 (tmtt) REVERT: F 214 ASN cc_start: 0.2366 (OUTLIER) cc_final: 0.1744 (t0) outliers start: 93 outliers final: 55 residues processed: 292 average time/residue: 0.4377 time to fit residues: 212.9552 Evaluate side-chains 245 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 184 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain Y residue 215 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain F residue 215 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 168 optimal weight: 0.9980 chunk 200 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 265 optimal weight: 0.5980 chunk 170 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 300 optimal weight: 40.0000 chunk 209 optimal weight: 1.9990 chunk 306 optimal weight: 0.0470 chunk 356 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 203 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 = 0.4641 r_free = 0.4641 target = 0.191314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.165165 restraints weight = 66814.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.159075 restraints weight = 88307.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.154070 restraints weight = 96616.233| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34717 Z= 0.117 Angle : 0.617 11.094 47327 Z= 0.308 Chirality : 0.045 0.241 5433 Planarity : 0.004 0.060 6072 Dihedral : 8.131 96.726 5198 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.45 % Allowed : 13.79 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -1.61 (0.13), residues: 4266 helix: 1.36 (0.20), residues: 665 sheet: -0.73 (0.14), residues: 1227 loop : -2.04 (0.12), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Y 47 HIS 0.005 0.001 HIS C1048 PHE 0.038 0.001 PHE B 135 TYR 0.021 0.001 TYR C 200 ARG 0.011 0.000 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 27) link_NAG-ASN : angle 2.46166 ( 81) hydrogen bonds : bond 0.04310 ( 1273) hydrogen bonds : angle 5.70824 ( 3495) SS BOND : bond 0.00342 ( 49) SS BOND : angle 1.54705 ( 98) covalent geometry : bond 0.00262 (34641) covalent geometry : angle 0.60538 (47148) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 207 time to evaluate : 4.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 ASP cc_start: 0.5408 (p0) cc_final: 0.5061 (p0) REVERT: B 343 ASN cc_start: 0.6203 (m-40) cc_final: 0.5803 (t0) REVERT: B 660 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.7531 (m-80) REVERT: B 977 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7615 (pp) REVERT: C 950 ASP cc_start: 0.6958 (p0) cc_final: 0.6724 (p0) REVERT: C 1063 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8042 (pp) REVERT: C 1107 ARG cc_start: 0.8005 (ttm170) cc_final: 0.7698 (mtt90) REVERT: L 65 ASP cc_start: 0.6173 (m-30) cc_final: 0.5909 (m-30) REVERT: H 102 MET cc_start: 0.4462 (pmm) cc_final: 0.3878 (pmm) REVERT: H 134 LYS cc_start: 0.3035 (ttpp) cc_final: 0.2402 (ptpt) REVERT: H 160 LYS cc_start: 0.2594 (mttm) cc_final: 0.1697 (pttm) REVERT: Y 101 GLU cc_start: 0.5200 (OUTLIER) cc_final: 0.4168 (mp0) REVERT: E 35 TYR cc_start: 0.1994 (OUTLIER) cc_final: 0.1259 (t80) REVERT: F 43 LYS cc_start: 0.3384 (mmtm) cc_final: 0.2160 (tmtt) REVERT: F 214 ASN cc_start: 0.2171 (OUTLIER) cc_final: 0.1626 (t0) outliers start: 92 outliers final: 58 residues processed: 286 average time/residue: 0.5733 time to fit residues: 278.3158 Evaluate side-chains 253 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 189 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 214 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 71.187 > 50: distance: 8 - 14: 6.988 distance: 14 - 15: 13.627 distance: 15 - 16: 13.384 distance: 15 - 18: 15.838 distance: 16 - 17: 31.758 distance: 16 - 20: 18.785 distance: 18 - 19: 25.633 distance: 20 - 21: 31.522 distance: 21 - 22: 49.979 distance: 21 - 24: 19.265 distance: 22 - 23: 21.805 distance: 22 - 28: 25.220 distance: 24 - 25: 37.264 distance: 25 - 26: 33.086 distance: 25 - 27: 38.787 distance: 28 - 29: 37.039 distance: 28 - 34: 26.914 distance: 29 - 30: 48.822 distance: 29 - 32: 56.658 distance: 30 - 31: 48.078 distance: 30 - 35: 33.420 distance: 32 - 33: 53.398 distance: 33 - 34: 41.109 distance: 35 - 36: 16.717 distance: 36 - 37: 20.148 distance: 36 - 39: 52.071 distance: 37 - 38: 30.677 distance: 37 - 42: 54.936 distance: 39 - 40: 26.585 distance: 39 - 41: 48.012 distance: 42 - 43: 18.180 distance: 43 - 44: 24.177 distance: 43 - 46: 8.013 distance: 44 - 45: 12.089 distance: 44 - 49: 50.665 distance: 46 - 47: 51.662 distance: 46 - 48: 48.724 distance: 49 - 50: 29.401 distance: 49 - 55: 29.888 distance: 50 - 51: 55.807 distance: 50 - 53: 13.987 distance: 51 - 52: 35.389 distance: 51 - 56: 33.510 distance: 53 - 54: 11.773 distance: 54 - 55: 50.339 distance: 56 - 57: 21.614 distance: 57 - 58: 55.725 distance: 58 - 59: 55.877 distance: 58 - 60: 16.009 distance: 60 - 61: 23.318 distance: 61 - 62: 40.260 distance: 61 - 64: 27.655 distance: 62 - 69: 8.955 distance: 64 - 65: 47.223 distance: 65 - 66: 15.619 distance: 66 - 67: 39.414 distance: 66 - 68: 36.019 distance: 69 - 70: 49.466 distance: 69 - 75: 31.557 distance: 70 - 71: 45.690 distance: 70 - 73: 23.761 distance: 71 - 72: 3.085 distance: 71 - 76: 30.314 distance: 74 - 75: 56.384 distance: 76 - 77: 26.000 distance: 76 - 101: 22.185 distance: 77 - 78: 15.565 distance: 77 - 80: 14.923 distance: 78 - 79: 27.204 distance: 78 - 81: 29.507 distance: 79 - 98: 35.753