Starting phenix.real_space_refine on Wed Jun 25 14:24:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zce_14628/06_2025/7zce_14628.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zce_14628/06_2025/7zce_14628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zce_14628/06_2025/7zce_14628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zce_14628/06_2025/7zce_14628.map" model { file = "/net/cci-nas-00/data/ceres_data/7zce_14628/06_2025/7zce_14628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zce_14628/06_2025/7zce_14628.cif" } resolution = 3.5 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= 0.001 sd= 0.105 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 123 5.16 5 C 18753 2.51 5 N 4849 2.21 5 O 5777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 1.88s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29502 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7897 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 55, 'TRANS': 955} Chain breaks: 7 Chain: "B" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7891 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 55, 'TRANS': 954} Chain breaks: 7 Chain: "C" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7891 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 55, 'TRANS': 954} Chain breaks: 7 Chain: "E" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1703 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 Chain: "F" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1703 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 Chain: "G" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1703 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: "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: "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: 19.58, per 1000 atoms: 0.66 Number of scatterers: 29502 At special positions: 0 Unit cell: (138.684, 142.24, 224.028, 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 123 16.00 O 5777 8.00 N 4849 7.00 C 18753 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 166 " distance=2.03 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=2.03 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 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 166 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 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 C 132 " - 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 391 " - pdb=" SG CYS C 525 " 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=2.03 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=2.02 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=2.03 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 E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 222 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 156 " - pdb=" SG CYS F 222 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 156 " - pdb=" SG CYS G 222 " 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 61 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 123 " " NAG A1309 " - " ASN A 343 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 61 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 123 " " NAG B1309 " - " ASN B 343 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 282 " " NAG C1307 " - " ASN C 123 " " NAG C1308 " - " ASN C 61 " " NAG C1309 " - " ASN C 343 " " NAG D 1 " - " ASN A 717 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN C 801 " Time building additional restraints: 8.51 Conformation dependent library (CDL) restraints added in 3.9 seconds 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6890 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 58 sheets defined 20.2% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.86 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.771A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.238A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.521A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.778A pdb=" N SER A 443 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 747 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 760 through 783 removed outlier: 4.095A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.980A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.679A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.763A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.908A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.618A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.667A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.029A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.599A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 removed outlier: 3.773A pdb=" N SER B 443 " --> pdb=" O ASN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.795A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.542A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.440A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.175A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.305A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.544A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.648A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.150A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.632A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.713A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.771A 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 removed outlier: 3.741A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 890' Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.881A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.750A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 988 Processing helix chain 'C' and resid 989 through 1033 Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 3.991A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 103 removed outlier: 4.155A pdb=" N GLY E 103 " --> pdb=" O SER E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 217 removed outlier: 3.814A pdb=" N PHE E 217 " --> pdb=" O PRO E 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 217 removed outlier: 4.042A pdb=" N PHE F 217 " --> pdb=" O PRO F 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 217 removed outlier: 3.910A pdb=" N PHE G 217 " --> pdb=" O PRO G 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.692A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 51 removed outlier: 4.026A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.717A pdb=" N LEU A 85 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 106 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 127 through 128 removed outlier: 4.054A pdb=" N VAL A 127 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 172 " --> pdb=" O VAL A 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 131 through 132 removed outlier: 3.692A pdb=" N PHE A 168 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.999A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.636A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.502A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 583 through 586 removed outlier: 4.569A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.978A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 719 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 719 removed outlier: 7.103A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.785A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.737A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.712A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.953A pdb=" N LEU B 85 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.770A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 327 removed outlier: 6.775A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.625A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.235A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.777A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.631A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.589A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.790A pdb=" N VAL B1133 " --> pdb=" O ALA B1080 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.912A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.278A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.844A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.747A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 328 removed outlier: 4.041A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.584A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.514A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.264A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 728 removed outlier: 7.091A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.654A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF2, first strand: chain 'E' and resid 18 through 19 removed outlier: 3.576A pdb=" N THR E 68 " --> pdb=" O GLN E 81 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.387A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR E 33 " --> pdb=" O ASP E 98 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 137 through 139 removed outlier: 3.506A pdb=" N ALA E 152 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP E 204 " --> pdb=" O SER E 201 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 187 through 188 removed outlier: 3.808A pdb=" N SER E 187 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP E 169 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TYR E 183 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU E 167 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL E 219 " --> pdb=" O GLN E 172 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR E 231 " --> pdb=" O GLN E 224 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 18 through 20 removed outlier: 3.757A pdb=" N LEU F 80 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR F 68 " --> pdb=" O GLN F 81 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 57 through 59 removed outlier: 3.646A pdb=" N SER F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR F 33 " --> pdb=" O ASP F 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 137 through 139 removed outlier: 3.505A pdb=" N ALA F 152 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE F 209 " --> pdb=" O ALA F 152 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 187 through 188 removed outlier: 3.995A pdb=" N SER F 187 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP F 169 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR F 183 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU F 167 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR F 231 " --> pdb=" O GLN F 224 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 18 through 20 removed outlier: 3.562A pdb=" N LEU G 80 " --> pdb=" O LEU G 20 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.305A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR G 33 " --> pdb=" O ASP G 98 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 137 through 139 removed outlier: 3.634A pdb=" N ALA G 152 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE G 209 " --> pdb=" O ALA G 152 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 187 through 188 removed outlier: 3.876A pdb=" N SER G 187 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TRP G 169 " --> pdb=" O LEU G 181 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N TYR G 183 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU G 167 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR G 231 " --> pdb=" O GLN G 224 " (cutoff:3.500A) 941 hydrogen bonds defined for protein. 2580 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: 16.32 Time building geometry restraints manager: 9.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 4779 1.26 - 1.40: 7528 1.40 - 1.54: 17599 1.54 - 1.68: 97 1.68 - 1.82: 153 Bond restraints: 30156 Sorted by residual: bond pdb=" CG PRO E 53 " pdb=" CD PRO E 53 " ideal model delta sigma weight residual 1.503 1.123 0.380 3.40e-02 8.65e+02 1.25e+02 bond pdb=" CB PRO E 53 " pdb=" CG PRO E 53 " ideal model delta sigma weight residual 1.492 1.141 0.351 5.00e-02 4.00e+02 4.94e+01 bond pdb=" C PRO F 174 " pdb=" N GLY F 175 " ideal model delta sigma weight residual 1.333 1.380 -0.047 1.43e-02 4.89e+03 1.08e+01 bond pdb=" C PRO G 174 " pdb=" N GLY G 175 " ideal model delta sigma weight residual 1.333 1.380 -0.047 1.57e-02 4.06e+03 8.95e+00 bond pdb=" C PRO E 174 " pdb=" N GLY E 175 " ideal model delta sigma weight residual 1.331 1.373 -0.041 1.46e-02 4.69e+03 7.99e+00 ... (remaining 30151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.55: 41024 9.55 - 19.09: 3 19.09 - 28.64: 2 28.64 - 38.18: 0 38.18 - 47.73: 1 Bond angle restraints: 41030 Sorted by residual: angle pdb=" N PRO E 53 " pdb=" CD PRO E 53 " pdb=" CG PRO E 53 " ideal model delta sigma weight residual 103.20 76.11 27.09 1.50e+00 4.44e-01 3.26e+02 angle pdb=" CB PRO E 53 " pdb=" CG PRO E 53 " pdb=" CD PRO E 53 " ideal model delta sigma weight residual 106.10 153.83 -47.73 3.20e+00 9.77e-02 2.22e+02 angle pdb=" CA PRO E 53 " pdb=" CB PRO E 53 " pdb=" CG PRO E 53 " ideal model delta sigma weight residual 104.50 78.70 25.80 1.90e+00 2.77e-01 1.84e+02 angle pdb=" CA PRO E 53 " pdb=" N PRO E 53 " pdb=" CD PRO E 53 " ideal model delta sigma weight residual 112.00 102.21 9.79 1.40e+00 5.10e-01 4.89e+01 angle pdb=" CA PRO F 193 " pdb=" N PRO F 193 " pdb=" CD PRO F 193 " ideal model delta sigma weight residual 112.00 105.81 6.19 1.40e+00 5.10e-01 1.95e+01 ... (remaining 41025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.06: 17351 23.06 - 46.11: 1057 46.11 - 69.17: 140 69.17 - 92.22: 44 92.22 - 115.28: 39 Dihedral angle restraints: 18631 sinusoidal: 7894 harmonic: 10737 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -167.53 81.53 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 169.09 -76.09 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual -86.00 -14.83 -71.17 1 1.00e+01 1.00e-02 6.50e+01 ... (remaining 18628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4118 0.066 - 0.132: 641 0.132 - 0.198: 29 0.198 - 0.264: 2 0.264 - 0.330: 2 Chirality restraints: 4792 Sorted by residual: chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 4789 not shown) Planarity restraints: 5287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 82 " 0.072 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO C 83 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO C 83 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 83 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 192 " -0.061 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO F 193 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO F 193 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 193 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 52 " -0.050 5.00e-02 4.00e+02 6.94e-02 7.72e+00 pdb=" N PRO E 53 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO E 53 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 53 " -0.038 5.00e-02 4.00e+02 ... (remaining 5284 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 336 2.64 - 3.21: 26239 3.21 - 3.77: 42052 3.77 - 4.34: 56607 4.34 - 4.90: 95397 Nonbonded interactions: 220631 Sorted by model distance: nonbonded pdb=" OH TYR B 756 " pdb=" OD2 ASP B 994 " model vdw 2.080 3.040 nonbonded pdb=" O LEU A 455 " pdb=" OH TYR G 33 " model vdw 2.117 3.040 nonbonded pdb=" OH TYR C 421 " pdb=" O PRO E 53 " model vdw 2.174 3.040 nonbonded pdb=" O LEU B 455 " pdb=" OH TYR F 33 " model vdw 2.178 3.040 nonbonded pdb=" OD1 ASN C 280 " pdb=" OG1 THR C 286 " model vdw 2.202 3.040 ... (remaining 220626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 1146 or resid 1301 through 1309)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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=0.50 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: 4.910 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: 1.260 Check model and map are aligned: 0.260 Set scattering table: 0.290 Process input model: 76.030 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.210 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 : 0.005 0.380 30251 Z= 0.190 Angle : 0.717 47.728 41271 Z= 0.364 Chirality : 0.046 0.330 4792 Planarity : 0.005 0.107 5248 Dihedral : 15.542 115.277 11609 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.03 % Allowed : 0.47 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.09 (0.14), residues: 3646 helix: 2.46 (0.22), residues: 583 sheet: 0.05 (0.18), residues: 886 loop : -2.11 (0.12), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 886 HIS 0.009 0.001 HIS C 207 PHE 0.029 0.001 PHE C 906 TYR 0.017 0.001 TYR E 52 ARG 0.005 0.000 ARG C 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 39) link_NAG-ASN : angle 2.57385 ( 117) link_BETA1-4 : bond 0.00422 ( 12) link_BETA1-4 : angle 1.81405 ( 36) hydrogen bonds : bond 0.14261 ( 939) hydrogen bonds : angle 5.87151 ( 2580) SS BOND : bond 0.00281 ( 44) SS BOND : angle 1.35667 ( 88) covalent geometry : bond 0.00472 (30156) covalent geometry : angle 0.70067 (41030) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 TYR cc_start: 0.7022 (m-80) cc_final: 0.6257 (m-80) REVERT: C 123 ASN cc_start: 0.4455 (p0) cc_final: 0.4216 (p0) REVERT: E 38 ARG cc_start: 0.3949 (ttm170) cc_final: 0.3512 (ttt-90) REVERT: E 86 ARG cc_start: 0.4310 (ptt180) cc_final: 0.3735 (tpp80) REVERT: E 169 TRP cc_start: 0.7123 (m100) cc_final: 0.6547 (m-10) REVERT: G 66 ARG cc_start: 0.2448 (ptt180) cc_final: 0.1807 (tpt90) REVERT: G 82 MET cc_start: 0.0145 (mmt) cc_final: -0.1060 (mmm) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.4658 time to fit residues: 150.6087 Evaluate side-chains 147 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 20.0000 chunk 279 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 289 optimal weight: 0.9980 chunk 111 optimal weight: 20.0000 chunk 175 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 335 optimal weight: 40.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN E 3 GLN E 110 GLN F 73 ASN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.178896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.108134 restraints weight = 53778.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.109559 restraints weight = 34741.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109041 restraints weight = 23644.602| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30251 Z= 0.138 Angle : 0.627 12.890 41271 Z= 0.306 Chirality : 0.046 0.367 4792 Planarity : 0.005 0.071 5248 Dihedral : 10.521 106.469 5053 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 0.47 % Allowed : 6.85 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.09 (0.14), residues: 3646 helix: 2.45 (0.22), residues: 584 sheet: -0.07 (0.17), residues: 936 loop : -2.10 (0.13), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 353 HIS 0.004 0.001 HIS C1058 PHE 0.018 0.001 PHE C 906 TYR 0.018 0.001 TYR B1067 ARG 0.010 0.000 ARG G 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 39) link_NAG-ASN : angle 2.53338 ( 117) link_BETA1-4 : bond 0.00592 ( 12) link_BETA1-4 : angle 1.84245 ( 36) hydrogen bonds : bond 0.05120 ( 939) hydrogen bonds : angle 5.14079 ( 2580) SS BOND : bond 0.00283 ( 44) SS BOND : angle 1.17570 ( 88) covalent geometry : bond 0.00325 (30156) covalent geometry : angle 0.60932 (41030) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 ASP cc_start: 0.7178 (t0) cc_final: 0.6930 (t0) REVERT: B 168 PHE cc_start: 0.6503 (t80) cc_final: 0.6184 (t80) REVERT: B 200 TYR cc_start: 0.7212 (m-80) cc_final: 0.6445 (m-80) REVERT: B 211 ASN cc_start: 0.5978 (m-40) cc_final: 0.5376 (m-40) REVERT: E 38 ARG cc_start: 0.3917 (ttm170) cc_final: 0.3477 (ttt-90) REVERT: E 86 ARG cc_start: 0.4242 (ptt180) cc_final: 0.3780 (tpp80) REVERT: G 82 MET cc_start: 0.0158 (mmt) cc_final: -0.0131 (mmm) REVERT: G 144 LEU cc_start: 0.0523 (pp) cc_final: -0.0547 (mp) outliers start: 15 outliers final: 10 residues processed: 181 average time/residue: 0.4885 time to fit residues: 142.6423 Evaluate side-chains 158 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 4.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain E residue 2 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 64.8529 > 50: distance: 4 - 9: 6.964 distance: 9 - 10: 15.801 distance: 10 - 11: 28.324 distance: 10 - 13: 9.464 distance: 11 - 12: 19.005 distance: 11 - 17: 22.271 distance: 13 - 14: 4.180 distance: 14 - 15: 5.233 distance: 14 - 16: 5.568 distance: 17 - 18: 9.362 distance: 18 - 19: 8.741 distance: 18 - 21: 4.912 distance: 19 - 20: 3.632 distance: 19 - 25: 25.861 distance: 21 - 22: 5.373 distance: 21 - 23: 6.737 distance: 22 - 24: 7.706 distance: 25 - 26: 21.329 distance: 26 - 27: 38.771 distance: 26 - 29: 15.338 distance: 27 - 28: 23.261 distance: 27 - 32: 27.659 distance: 29 - 30: 15.805 distance: 29 - 31: 10.421 distance: 32 - 33: 16.032 distance: 33 - 34: 34.671 distance: 33 - 36: 19.677 distance: 34 - 35: 36.347 distance: 34 - 40: 47.092 distance: 36 - 37: 18.352 distance: 37 - 38: 29.845 distance: 37 - 39: 24.856 distance: 40 - 41: 15.058 distance: 41 - 42: 46.047 distance: 41 - 44: 15.528 distance: 42 - 43: 19.686 distance: 42 - 48: 3.224 distance: 44 - 45: 32.928 distance: 45 - 46: 41.009 distance: 45 - 47: 39.572 distance: 48 - 49: 10.939 distance: 49 - 50: 50.464 distance: 49 - 52: 24.358 distance: 50 - 51: 11.783 distance: 50 - 54: 18.309 distance: 52 - 53: 44.932 distance: 53 - 124: 23.239 distance: 54 - 55: 34.329 distance: 54 - 60: 44.054 distance: 55 - 56: 30.834 distance: 55 - 58: 19.177 distance: 56 - 57: 58.009 distance: 56 - 61: 32.246 distance: 57 - 85: 32.954 distance: 58 - 59: 35.407 distance: 59 - 60: 23.219 distance: 61 - 62: 25.890 distance: 62 - 63: 25.509 distance: 62 - 65: 31.392 distance: 63 - 64: 16.891 distance: 63 - 72: 31.720 distance: 64 - 92: 24.795 distance: 65 - 66: 12.998 distance: 66 - 67: 31.282 distance: 66 - 68: 33.638 distance: 67 - 69: 35.921 distance: 68 - 70: 41.755 distance: 69 - 71: 31.519 distance: 70 - 71: 46.554 distance: 72 - 73: 19.511 distance: 73 - 74: 25.180 distance: 74 - 75: 52.441 distance: 74 - 76: 31.152 distance: 75 - 103: 27.915 distance: 76 - 77: 22.989 distance: 77 - 78: 25.355 distance: 77 - 80: 34.687 distance: 78 - 79: 19.348 distance: 78 - 85: 16.472 distance: 80 - 81: 40.143 distance: 81 - 82: 29.722 distance: 82 - 83: 35.347 distance: 82 - 84: 34.091