Starting phenix.real_space_refine on Mon Aug 25 00:10:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9au2_43842/08_2025/9au2_43842.cif Found real_map, /net/cci-nas-00/data/ceres_data/9au2_43842/08_2025/9au2_43842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9au2_43842/08_2025/9au2_43842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9au2_43842/08_2025/9au2_43842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9au2_43842/08_2025/9au2_43842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9au2_43842/08_2025/9au2_43842.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.069 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 109 5.16 5 C 15130 2.51 5 N 4115 2.21 5 O 4391 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23745 Number of models: 1 Model: "" Number of chains: 20 Chain: "D" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 595 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 371 Unresolved non-hydrogen angles: 488 Unresolved non-hydrogen dihedrals: 320 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 6, 'PHE:plan': 3, 'TYR:plan': 13, 'TRP:plan': 3, 'ASP:plan': 7, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 228 Chain: "F" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 596 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 487 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 6, 'PHE:plan': 3, 'TYR:plan': 13, 'TRP:plan': 3, 'ASP:plan': 7, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 228 Chain: "I" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 541 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 3, 'ASP:plan': 6, 'TYR:plan': 8, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 172 Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 545 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 3, 'ASP:plan': 6, 'TYR:plan': 8, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 172 Chain: "A" Number of atoms: 7064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7064 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 220} Link IDs: {'PTRANS': 53, 'TRANS': 924} Chain breaks: 13 Unresolved non-hydrogen bonds: 636 Unresolved non-hydrogen angles: 815 Unresolved non-hydrogen dihedrals: 490 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 26, 'ASN:plan1': 14, 'PHE:plan': 4, 'GLU:plan': 20, 'TYR:plan': 7, 'ARG:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 336 Chain: "B" Number of atoms: 6854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 6854 Classifications: {'peptide': 977} Incomplete info: {'truncation_to_alanine': 272} Link IDs: {'PTRANS': 55, 'TRANS': 921} Chain breaks: 14 Unresolved non-hydrogen bonds: 862 Unresolved non-hydrogen angles: 1108 Unresolved non-hydrogen dihedrals: 691 Unresolved non-hydrogen chiralities: 90 Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 14, 'ASP:plan': 25, 'ASN:plan1': 19, 'ARG:plan': 8, 'PHE:plan': 10, 'GLU:plan': 19, 'HIS:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 478 Chain: "C" Number of atoms: 6864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 6864 Classifications: {'peptide': 1008} Incomplete info: {'truncation_to_alanine': 343} Link IDs: {'PTRANS': 52, 'TRANS': 955} Chain breaks: 13 Unresolved non-hydrogen bonds: 1097 Unresolved non-hydrogen angles: 1419 Unresolved non-hydrogen dihedrals: 886 Unresolved non-hydrogen chiralities: 114 Planarities with less than four sites: {'PHE:plan': 17, 'GLN:plan1': 15, 'GLU:plan': 25, 'ASN:plan1': 23, 'ASP:plan': 30, 'ARG:plan': 10, 'HIS:plan': 4, 'TYR:plan': 16, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 630 Chain: "E" 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: "G" 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: "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: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 4.95, per 1000 atoms: 0.21 Number of scatterers: 23745 At special positions: 0 Unit cell: (134, 144, 213, 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 109 16.00 O 4391 8.00 N 4115 7.00 C 15130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 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 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 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 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=2.03 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 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 E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 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-ASN " NAG A1501 " - " ASN A 717 " " NAG A1502 " - " ASN A1134 " " NAG A1503 " - " ASN A 282 " " NAG A1504 " - " ASN A 616 " " NAG A1505 " - " ASN A 709 " " NAG A1506 " - " ASN A1074 " " NAG A1507 " - " ASN A 343 " " NAG A1508 " - " ASN A 354 " " NAG A1509 " - " ASN A 657 " " NAG A1510 " - " ASN A 603 " " NAG A1511 " - " ASN A 62 " " NAG A1512 " - " ASN A 331 " " NAG A1513 " - " ASN A 234 " " NAG A1514 " - " ASN A 165 " " NAG B1501 " - " ASN B 616 " " NAG B1502 " - " ASN B1074 " " NAG B1503 " - " ASN B 282 " " NAG B1504 " - " ASN B 709 " " NAG C1501 " - " ASN C 282 " " NAG C1502 " - " ASN C1098 " " NAG C1503 " - " ASN C 234 " " NAG C1504 " - " ASN C 122 " " NAG C1505 " - " ASN C 331 " " NAG C1506 " - " ASN C 709 " " NAG C1507 " - " ASN C1134 " " NAG C1508 " - " ASN C 165 " " NAG C1509 " - " ASN C 62 " " NAG C1510 " - " ASN C1074 " " NAG C1511 " - " ASN C 616 " " NAG E 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 801 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B 331 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C 245 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6380 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 58 sheets defined 22.3% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.752A pdb=" N GLU I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.824A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.910A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.620A pdb=" N PHE A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.457A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.634A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.673A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.534A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.514A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) 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 removed outlier: 3.531A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.876A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.617A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.703A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.637A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.726A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.088A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.939A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 626 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.615A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.523A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.574A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.540A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.749A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.574A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.709A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 627 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.630A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) 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 758 through 783 removed outlier: 3.695A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.515A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.843A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.584A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.515A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.188A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.662A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.555A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.517A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.624A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.081A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 112 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.081A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.574A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N TYR F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL F 112 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.574A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N TYR F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 9 through 10 removed outlier: 6.860A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 9 through 10 removed outlier: 5.993A pdb=" N ILE I 98 " --> pdb=" O ALA I 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AB1, first strand: chain 'J' and resid 9 through 10 removed outlier: 6.220A pdb=" N GLN J 39 " --> pdb=" O PHE J 48 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N PHE J 48 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 9 through 10 removed outlier: 5.990A pdb=" N ILE J 98 " --> pdb=" O ALA J 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 17 through 23 Processing sheet with id=AB4, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.723A pdb=" N THR A 64 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 43 through 44 removed outlier: 4.290A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 43 through 44 removed outlier: 4.290A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 48 through 56 removed outlier: 3.728A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.927A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.666A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.078A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.519A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.685A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.628A pdb=" N VAL A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AC7, first strand: chain 'A' and resid 711 through 722 removed outlier: 6.722A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 725 through 728 removed outlier: 3.748A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.460A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.618A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.534A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 37 through 38 removed outlier: 7.063A pdb=" N VAL B 37 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 49 through 56 removed outlier: 3.673A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.569A pdb=" N VAL B 267 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 229 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 168 through 172 removed outlier: 3.854A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.885A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 609 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD9, first strand: chain 'B' and resid 361 through 362 removed outlier: 3.674A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.656A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.235A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE B 565 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.032A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.288A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.574A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.574A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.496A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'C' and resid 24 through 31 removed outlier: 7.953A pdb=" N ASN C 62 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N TYR C 269 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 49 through 56 removed outlier: 6.867A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.586A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.623A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.855A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.783A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.303A pdb=" N PHE C 392 " --> pdb=" O VAL C 524 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.664A pdb=" N VAL C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.574A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.927A 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: 5.818A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.574A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.927A 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: 3.801A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG4, first strand: chain 'C' and resid 1120 through 1122 1121 hydrogen bonds defined for protein. 3009 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: 6.23 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4308 1.33 - 1.45: 6295 1.45 - 1.57: 13487 1.57 - 1.70: 0 1.70 - 1.82: 134 Bond restraints: 24224 Sorted by residual: bond pdb=" N PRO C 295 " pdb=" CD PRO C 295 " ideal model delta sigma weight residual 1.473 1.571 -0.098 1.40e-02 5.10e+03 4.90e+01 bond pdb=" N PRO A 295 " pdb=" CD PRO A 295 " ideal model delta sigma weight residual 1.473 1.568 -0.095 1.40e-02 5.10e+03 4.64e+01 bond pdb=" CA PHE C 92 " pdb=" C PHE C 92 " ideal model delta sigma weight residual 1.522 1.467 0.055 1.20e-02 6.94e+03 2.11e+01 bond pdb=" CA TYR C 91 " pdb=" C TYR C 91 " ideal model delta sigma weight residual 1.521 1.472 0.049 1.19e-02 7.06e+03 1.73e+01 bond pdb=" N ILE C 101 " pdb=" CA ILE C 101 " ideal model delta sigma weight residual 1.460 1.505 -0.045 1.23e-02 6.61e+03 1.35e+01 ... (remaining 24219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 32746 2.55 - 5.11: 403 5.11 - 7.66: 39 7.66 - 10.22: 3 10.22 - 12.77: 2 Bond angle restraints: 33193 Sorted by residual: angle pdb=" CA PRO I 57 " pdb=" N PRO I 57 " pdb=" CD PRO I 57 " ideal model delta sigma weight residual 112.00 99.23 12.77 1.40e+00 5.10e-01 8.32e+01 angle pdb=" C PHE C 86 " pdb=" CA PHE C 86 " pdb=" CB PHE C 86 " ideal model delta sigma weight residual 110.85 99.39 11.46 1.70e+00 3.46e-01 4.54e+01 angle pdb=" CA PHE C 92 " pdb=" CB PHE C 92 " pdb=" CG PHE C 92 " ideal model delta sigma weight residual 113.80 119.09 -5.29 1.00e+00 1.00e+00 2.79e+01 angle pdb=" CA GLY B 268 " pdb=" C GLY B 268 " pdb=" O GLY B 268 " ideal model delta sigma weight residual 121.57 117.09 4.48 8.70e-01 1.32e+00 2.65e+01 angle pdb=" N PHE C 92 " pdb=" CA PHE C 92 " pdb=" CB PHE C 92 " ideal model delta sigma weight residual 111.08 102.34 8.74 1.71e+00 3.42e-01 2.61e+01 ... (remaining 33188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14301 17.99 - 35.99: 485 35.99 - 53.98: 92 53.98 - 71.97: 15 71.97 - 89.96: 8 Dihedral angle restraints: 14901 sinusoidal: 5047 harmonic: 9854 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -142.63 56.63 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" C PHE C 86 " pdb=" N PHE C 86 " pdb=" CA PHE C 86 " pdb=" CB PHE C 86 " ideal model delta harmonic sigma weight residual -122.60 -109.20 -13.40 0 2.50e+00 1.60e-01 2.87e+01 dihedral pdb=" CA ASN C 165 " pdb=" C ASN C 165 " pdb=" N CYS C 166 " pdb=" CA CYS C 166 " ideal model delta harmonic sigma weight residual 180.00 153.85 26.15 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 14898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3608 0.084 - 0.168: 417 0.168 - 0.252: 29 0.252 - 0.336: 3 0.336 - 0.420: 2 Chirality restraints: 4059 Sorted by residual: chirality pdb=" C1 NAG A1502 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG A1502 " pdb=" O5 NAG A1502 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CA ASP C 41 " pdb=" N ASP C 41 " pdb=" C ASP C 41 " pdb=" CB ASP C 41 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA VAL C 83 " pdb=" N VAL C 83 " pdb=" C VAL C 83 " pdb=" CB VAL C 83 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 4056 not shown) Planarity restraints: 4377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 102 " 0.467 9.50e-02 1.11e+02 2.09e-01 2.69e+01 pdb=" NE ARG C 102 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG C 102 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 102 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 102 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1502 " 0.047 2.00e-02 2.50e+03 3.85e-02 1.85e+01 pdb=" C7 NAG A1502 " -0.010 2.00e-02 2.50e+03 pdb=" C8 NAG A1502 " 0.035 2.00e-02 2.50e+03 pdb=" N2 NAG A1502 " -0.062 2.00e-02 2.50e+03 pdb=" O7 NAG A1502 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 634 " 0.371 9.50e-02 1.11e+02 1.66e-01 1.70e+01 pdb=" NE ARG C 634 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG C 634 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 634 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 634 " 0.011 2.00e-02 2.50e+03 ... (remaining 4374 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 94 2.60 - 3.18: 18602 3.18 - 3.75: 32941 3.75 - 4.33: 46579 4.33 - 4.90: 80072 Nonbonded interactions: 178288 Sorted by model distance: nonbonded pdb=" OG1 THR B 26 " pdb=" O HIS B 67 " model vdw 2.030 3.040 nonbonded pdb=" OE2 GLU C 819 " pdb=" OG SER C1055 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR A 38 " pdb=" O LEU A 55 " model vdw 2.236 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.248 3.040 nonbonded pdb=" OE2 GLU A 819 " pdb=" OG SER A1055 " model vdw 2.257 3.040 ... (remaining 178283 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 30 and (name N or name CA or name C or name O \ or name CB )) or resid 31 through 32 or (resid 33 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )) or resid 55 through 61 or (re \ sid 62 through 64 and (name N or name CA or name C or name O or name CB )) or re \ sid 65 through 69 or resid 82 through 95 or (resid 96 through 102 and (name N or \ name CA or name C or name O or name CB )) or resid 103 through 107 or (resid 11 \ 6 through 130 and (name N or name CA or name C or name O or name CB )) or resid \ 131 through 133 or resid 166 through 172 or (resid 173 and (name N or name CA or \ name C or name O or name CB )) or resid 174 through 176 or (resid 190 through 1 \ 91 and (name N or name CA or name C or name O or name CB )) or resid 192 or (res \ id 193 and (name N or name CA or name C or name O or name CB )) or resid 194 thr \ ough 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) \ or resid 200 through 209 or (resid 216 and (name N or name CA or name C or name \ O or name CB )) or resid 217 or (resid 218 and (name N or name CA or name C or n \ ame O or name CB )) or resid 219 through 232 or (resid 233 and (name N or name C \ A or name C or name O or name CB )) or resid 237 through 240 or resid 264 throug \ h 285 or (resid 286 through 288 and (name N or name CA or name C or name O or na \ me CB )) or resid 289 through 297 or (resid 298 and (name N or name CA or name C \ or name O or name CB )) or resid 299 through 306 or (resid 307 and (name N or n \ ame CA or name C or name O or name CB )) or resid 308 through 322 or (resid 323 \ through 327 and (name N or name CA or name C or name O or name CB )) or resid 32 \ 8 through 334 or (resid 335 and (name N or name CA or name C or name O or name C \ B )) or resid 336 through 337 or (resid 338 through 343 and (name N or name CA o \ r name C or name O or name CB )) or (resid 345 through 360 and (name N or name C \ A or name C or name O or name CB )) or resid 361 or (resid 362 through 369 and ( \ name N or name CA or name C or name O or name CB )) or resid 373 or (resid 374 t \ hrough 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ or (resid 380 and (name N or name CA or name C or name O or name CB )) or resid \ 381 or (resid 382 through 383 and (name N or name CA or name C or name O or nam \ e CB )) or resid 384 or (resid 385 through 390 and (name N or name CA or name C \ or name O or name CB )) or resid 391 or (resid 392 through 403 and (name N or na \ me CA or name C or name O or name CB )) or (resid 404 through 411 and (name N or \ name CA or name C or name O or name CB )) or resid 412 or (resid 414 through 41 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 416 or (resi \ d 417 through 425 and (name N or name CA or name C or name O or name CB )) or re \ sid 431 through 432 or (resid 433 through 446 and (name N or name CA or name C o \ r name O or name CB )) or (resid 447 through 462 and (name N or name CA or name \ C or name O or name CB )) or resid 463 or (resid 464 through 490 and (name N or \ name CA or name C or name O or name CB )) or resid 491 or (resid 492 through 495 \ and (name N or name CA or name C or name O or name CB )) or resid 496 or (resid \ 497 through 498 and (name N or name CA or name C or name O or name CB )) or res \ id 499 through 507 or (resid 508 through 516 and (name N or name CA or name C or \ name O or name CB )) or (resid 523 through 524 and (name N or name CA or name C \ or name O or name CB )) or resid 525 through 527 or (resid 528 through 532 and \ (name N or name CA or name C or name O or name CB )) or resid 533 or (resid 534 \ and (name N or name CA or name C or name O or name CB )) or resid 535 through 53 \ 8 or (resid 539 and (name N or name CA or name C or name O or name CB )) or resi \ d 540 through 543 or (resid 544 and (name N or name CA or name C or name O or na \ me CB )) or resid 545 through 546 or (resid 547 and (name N or name CA or name C \ or name O or name CB )) or resid 548 through 552 or (resid 553 through 556 and \ (name N or name CA or name C or name O or name CB )) or resid 557 through 577 or \ (resid 578 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 9 or (resid 580 through 584 and (name N or name CA or name C or name O or name C \ B )) or resid 585 through 587 or (resid 588 and (name N or name CA or name C or \ name O or name CB )) or resid 589 through 595 or (resid 596 and (name N or name \ CA or name C or name O or name CB )) or resid 597 through 614 or (resid 615 and \ (name N or name CA or name C or name O or name CB )) or resid 616 through 620 or \ (resid 621 and (name N or name CA or name C or name O or name CB )) or resid 62 \ 2 through 624 or (resid 625 through 627 and (name N or name CA or name C or name \ O or name CB )) or resid 628 through 634 or (resid 635 through 638 and (name N \ or name CA or name C or name O or name CB )) or resid 639 through 645 or (resid \ 646 through 647 and (name N or name CA or name C or name O or name CB )) or resi \ d 648 through 660 or (resid 661 and (name N or name CA or name C or name O or na \ me CB )) or resid 662 or (resid 663 and (name N or name CA or name C or name O o \ r name CB )) or resid 664 through 674 or (resid 675 and (name N or name CA or na \ me C or name O or name CB )) or resid 690 through 703 or (resid 704 and (name N \ or name CA or name C or name O or name CB )) or resid 705 through 707 or (resid \ 708 and (name N or name CA or name C or name O or name CB )) or resid 709 throug \ h 710 or (resid 711 and (name N or name CA or name C or name O or name CB )) or \ resid 712 through 738 or (resid 739 and (name N or name CA or name C or name O o \ r name CB )) or resid 740 through 745 or (resid 746 through 748 and (name N or n \ ame CA or name C or name O or name CB )) or resid 749 or (resid 750 and (name N \ or name CA or name C or name O or name CB )) or resid 751 through 757 or (resid \ 758 through 759 and (name N or name CA or name C or name O or name CB )) or resi \ d 760 through 789 or (resid 790 and (name N or name CA or name C or name O or na \ me CB )) or resid 791 through 802 or (resid 803 and (name N or name CA or name C \ or name O or name CB )) or resid 804 through 809 or (resid 810 through 811 and \ (name N or name CA or name C or name O or name CB )) or resid 812 or (resid 813 \ through 814 and (name N or name CA or name C or name O or name CB )) or resid 81 \ 5 or (resid 816 and (name N or name CA or name C or name O or name CB )) or resi \ d 817 through 824 or (resid 825 through 826 and (name N or name CA or name C or \ name O or name CB )) or resid 855 through 883 or (resid 884 and (name N or name \ CA or name C or name O or name CB )) or resid 885 through 886 or (resid 887 and \ (name N or name CA or name C or name O or name CB )) or resid 888 through 911 or \ (resid 912 and (name N or name CA or name C or name O or name CB )) or resid 91 \ 3 or (resid 914 and (name N or name CA or name C or name O or name CB )) or resi \ d 915 through 930 or (resid 931 and (name N or name CA or name C or name O or na \ me CB )) or resid 932 through 934 or (resid 935 through 937 and (name N or name \ CA or name C or name O or name CB )) or resid 938 or (resid 939 through 941 and \ (name N or name CA or name C or name O or name CB )) or resid 943 through 963 or \ (resid 964 and (name N or name CA or name C or name O or name CB )) or resid 96 \ 5 through 966 or (resid 967 through 968 and (name N or name CA or name C or name \ O or name CB )) or resid 969 through 973 or (resid 974 and (name N or name CA o \ r name C or name O or name CB )) or resid 975 through 990 or (resid 991 and (nam \ e N or name CA or name C or name O or name CB )) or resid 992 through 997 or (re \ sid 998 and (name N or name CA or name C or name O or name CB )) or resid 999 th \ rough 1001 or (resid 1002 through 1003 and (name N or name CA or name C or name \ O or name CB )) or resid 1004 through 1005 or (resid 1006 and (name N or name CA \ or name C or name O or name CB )) or resid 1007 through 1008 or (resid 1009 and \ (name N or name CA or name C or name O or name CB )) or resid 1010 through 1029 \ or (resid 1030 and (name N or name CA or name C or name O or name CB )) or resi \ d 1031 through 1037 or (resid 1038 and (name N or name CA or name C or name O or \ name CB )) or resid 1039 through 1050 or (resid 1051 and (name N or name CA or \ name C or name O or name CB )) or resid 1052 through 1054 or (resid 1055 through \ 1056 and (name N or name CA or name C or name O or name CB )) or resid 1057 thr \ ough 1093 or (resid 1094 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1095 through 1096 or (resid 1097 and (name N or name CA or name C or \ name O or name CB )) or resid 1098 through 1099 or (resid 1100 and (name N or na \ me CA or name C or name O or name CB )) or resid 1101 through 1110 or (resid 111 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 1112 through \ 1113 or (resid 1114 and (name N or name CA or name C or name O or name CB )) or \ resid 1115 or (resid 1116 and (name N or name CA or name C or name O or name CB \ )) or resid 1117 through 1135 or (resid 1136 and (name N or name CA or name C o \ r name O or name CB )) or resid 1137 through 1138 or (resid 1139 and (name N or \ name CA or name C or name O or name CB )) or resid 1140 through 1143 or resid 15 \ 04)) selection = (chain 'B' and (resid 27 through 32 or (resid 33 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 46 or (resid 47 through \ 48 and (name N or name CA or name C or name O or name CB )) or resid 49 through \ 62 or (resid 63 through 64 and (name N or name CA or name C or name O or name C \ B )) or resid 65 through 93 or (resid 94 through 102 and (name N or name CA or n \ ame C or name O or name CB )) or resid 103 through 119 or (resid 120 through 130 \ and (name N or name CA or name C or name O or name CB )) or resid 131 through 1 \ 66 or (resid 167 through 173 and (name N or name CA or name C or name O or name \ CB )) or resid 174 through 228 or (resid 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 through 240 or (resid 264 and (name N or name \ CA or name C or name O or name CB )) or resid 265 through 286 or (resid 287 thr \ ough 288 and (name N or name CA or name C or name O or name CB )) or resid 289 t \ hrough 297 or (resid 298 and (name N or name CA or name C or name O or name CB ) \ ) or resid 299 through 322 or (resid 323 through 327 and (name N or name CA or n \ ame C or name O or name CB )) or resid 328 through 337 or (resid 338 through 360 \ and (name N or name CA or name C or name O or name CB )) or resid 361 through 3 \ 63 or (resid 364 through 369 and (name N or name CA or name C or name O or name \ CB )) or resid 373 through 376 or (resid 377 through 378 and (name N or name CA \ or name C or name O or name CB )) or resid 379 through 391 or (resid 392 through \ 403 and (name N or name CA or name C or name O or name CB )) or resid 404 throu \ gh 425 or resid 431 through 435 or (resid 436 through 446 and (name N or name CA \ or name C or name O or name CB )) or resid 447 through 457 or resid 459 through \ 470 or resid 489 through 493 or (resid 494 through 495 and (name N or name CA o \ r name C or name O or name CB )) or resid 496 through 505 or (resid 506 and (nam \ e N or name CA or name C or name O or name CB )) or resid 507 through 508 or (re \ sid 509 through 516 and (name N or name CA or name C or name O or name CB )) or \ resid 523 through 527 or (resid 528 through 532 and (name N or name CA or name C \ or name O or name CB )) or resid 533 through 538 or (resid 539 and (name N or n \ ame CA or name C or name O or name CB )) or resid 540 through 543 or (resid 544 \ and (name N or name CA or name C or name O or name CB )) or resid 545 through 54 \ 8 or (resid 549 and (name N or name CA or name C or name O or name CB )) or resi \ d 550 through 553 or (resid 554 through 556 and (name N or name CA or name C or \ name O or name CB )) or resid 557 through 567 or (resid 568 through 572 and (nam \ e N or name CA or name C or name O or name CB )) or resid 573 through 575 or (re \ sid 576 and (name N or name CA or name C or name O or name CB )) or resid 577 or \ (resid 578 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 9 or (resid 580 through 584 and (name N or name CA or name C or name O or name C \ B )) or resid 585 through 590 or (resid 591 and (name N or name CA or name C or \ name O or name CB )) or resid 592 through 603 or (resid 604 through 605 and (nam \ e N or name CA or name C or name O or name CB )) or resid 606 through 614 or (re \ sid 615 and (name N or name CA or name C or name O or name CB )) or resid 616 th \ rough 617 or (resid 618 through 619 and (name N or name CA or name C or name O o \ r name CB )) or resid 620 through 624 or (resid 625 through 627 and (name N or n \ ame CA or name C or name O or name CB )) or resid 628 through 636 or (resid 637 \ through 638 and (name N or name CA or name C or name O or name CB )) or resid 63 \ 9 through 644 or (resid 645 through 647 and (name N or name CA or name C or name \ O or name CB )) or resid 648 through 653 or (resid 654 and (name N or name CA o \ r name C or name O or name CB )) or resid 655 through 657 or (resid 658 through \ 659 and (name N or name CA or name C or name O or name CB )) or resid 660 throug \ h 662 or (resid 663 and (name N or name CA or name C or name O or name CB )) or \ resid 664 through 690 or (resid 691 and (name N or name CA or name C or name O o \ r name CB )) or resid 692 through 701 or (resid 702 and (name N or name CA or na \ me C or name O or name CB )) or resid 703 through 720 or (resid 721 and (name N \ or name CA or name C or name O or name CB )) or resid 722 or (resid 723 and (nam \ e N or name CA or name C or name O or name CB )) or resid 724 through 734 or (re \ sid 735 and (name N or name CA or name C or name O or name CB )) or resid 736 th \ rough 738 or (resid 739 and (name N or name CA or name C or name O or name CB )) \ or resid 740 through 744 or (resid 745 through 748 and (name N or name CA or na \ me C or name O or name CB )) or resid 749 through 758 or (resid 759 and (name N \ or name CA or name C or name O or name CB )) or resid 760 through 775 or (resid \ 776 and (name N or name CA or name C or name O or name CB )) or resid 777 throug \ h 815 or (resid 816 and (name N or name CA or name C or name O or name CB )) or \ resid 817 through 824 or (resid 825 through 826 and (name N or name CA or name C \ or name O or name CB )) or resid 855 through 858 or (resid 859 and (name N or n \ ame CA or name C or name O or name CB )) or resid 860 through 865 or (resid 866 \ through 868 and (name N or name CA or name C or name O or name CB )) or resid 86 \ 9 through 883 or (resid 884 and (name N or name CA or name C or name O or name C \ B )) or resid 885 through 886 or (resid 887 and (name N or name CA or name C or \ name O or name CB )) or resid 888 through 911 or (resid 912 and (name N or name \ CA or name C or name O or name CB )) or resid 913 or (resid 914 and (name N or n \ ame CA or name C or name O or name CB )) or resid 915 through 920 or (resid 921 \ and (name N or name CA or name C or name O or name CB )) or resid 922 through 93 \ 0 or (resid 931 and (name N or name CA or name C or name O or name CB )) or resi \ d 932 through 934 or (resid 935 through 937 and (name N or name CA or name C or \ name O or name CB )) or resid 938 through 941 or resid 943 through 950 or (resid \ 951 and (name N or name CA or name C or name O or name CB )) or resid 952 throu \ gh 967 or (resid 968 and (name N or name CA or name C or name O or name CB )) or \ resid 969 through 972 or (resid 973 through 974 and (name N or name CA or name \ C or name O or name CB )) or resid 975 through 977 or (resid 978 through 979 and \ (name N or name CA or name C or name O or name CB )) or resid 980 through 982 o \ r (resid 983 through 985 and (name N or name CA or name C or name O or name CB ) \ ) or resid 986 through 990 or (resid 991 and (name N or name CA or name C or nam \ e O or name CB )) or resid 992 through 997 or (resid 998 and (name N or name CA \ or name C or name O or name CB )) or resid 999 through 1005 or (resid 1006 and ( \ name N or name CA or name C or name O or name CB )) or resid 1007 through 1008 o \ r (resid 1009 and (name N or name CA or name C or name O or name CB )) or resid \ 1010 through 1029 or (resid 1030 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1031 through 1037 or (resid 1038 and (name N or name CA or na \ me C or name O or name CB )) or resid 1039 through 1050 or (resid 1051 and (name \ N or name CA or name C or name O or name CB )) or resid 1052 through 1071 or (r \ esid 1072 and (name N or name CA or name C or name O or name CB )) or resid 1073 \ through 1093 or (resid 1094 and (name N or name CA or name C or name O or name \ CB )) or resid 1095 through 1110 or (resid 1111 and (name N or name CA or name C \ or name O or name CB )) or resid 1112 through 1113 or (resid 1114 and (name N o \ r name CA or name C or name O or name CB )) or resid 1115 through 1124 or (resid \ 1125 and (name N or name CA or name C or name O or name CB )) or resid 1126 thr \ ough 1143 or resid 1504)) selection = (chain 'C' and ((resid 27 through 30 and (name N or name CA or name C or name O \ or name CB )) or resid 31 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 47 or (resid 48 and (name N or na \ me CA or name C or name O or name CB )) or resid 49 through 53 or (resid 54 and \ (name N or name CA or name C or name O or name CB )) or resid 55 through 61 or ( \ resid 62 through 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 69 or resid 82 through 87 or (resid 88 and (name N or name CA o \ r name C or name O or name CB )) or resid 89 or (resid 90 and (name N or name CA \ or name C or name O or name CB )) or resid 91 through 100 or (resid 101 through \ 102 and (name N or name CA or name C or name O or name CB )) or resid 103 throu \ gh 104 or (resid 105 and (name N or name CA or name C or name O or name CB )) or \ resid 106 through 107 or (resid 116 through 130 and (name N or name CA or name \ C or name O or name CB )) or resid 131 through 132 or (resid 133 and (name N or \ name CA or name C or name O or name CB )) or resid 166 through 167 or (resid 168 \ through 173 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 74 through 175 or (resid 176 and (name N or name CA or name C or name O or name \ CB )) or (resid 190 through 191 and (name N or name CA or name C or name O or na \ me CB )) or resid 192 or (resid 193 and (name N or name CA or name C or name O o \ r name CB )) or resid 194 through 195 or (resid 196 and (name N or name CA or na \ me C or name O or name CB )) or resid 200 through 209 or (resid 216 and (name N \ or name CA or name C or name O or name CB )) or resid 217 through 228 or (resid \ 229 and (name N or name CA or name C or name O or name CB )) or resid 230 throug \ h 232 or (resid 233 and (name N or name CA or name C or name O or name CB )) or \ resid 237 through 238 or (resid 239 through 240 and (name N or name CA or name C \ or name O or name CB )) or resid 264 through 266 or (resid 267 and (name N or n \ ame CA or name C or name O or name CB )) or resid 268 through 306 or (resid 307 \ and (name N or name CA or name C or name O or name CB )) or resid 308 through 31 \ 5 or (resid 316 and (name N or name CA or name C or name O or name CB )) or resi \ d 317 through 343 or resid 345 through 412 or resid 414 through 457 or resid 459 \ through 470 or resid 489 through 575 or (resid 576 and (name N or name CA or na \ me C or name O or name CB )) or resid 577 through 595 or (resid 596 and (name N \ or name CA or name C or name O or name CB )) or resid 597 through 603 or (resid \ 604 through 605 and (name N or name CA or name C or name O or name CB )) or resi \ d 606 through 618 or (resid 619 and (name N or name CA or name C or name O or na \ me CB )) or resid 620 through 629 or (resid 630 and (name N or name CA or name C \ or name O or name CB )) or resid 631 through 634 or (resid 635 through 638 and \ (name N or name CA or name C or name O or name CB )) or resid 639 through 657 or \ (resid 658 through 659 and (name N or name CA or name C or name O or name CB )) \ or resid 660 through 710 or (resid 711 and (name N or name CA or name C or name \ O or name CB )) or resid 712 through 720 or (resid 721 and (name N or name CA o \ r name C or name O or name CB )) or resid 722 through 775 or (resid 776 and (nam \ e N or name CA or name C or name O or name CB )) or resid 777 through 789 or (re \ sid 790 and (name N or name CA or name C or name O or name CB )) or resid 791 th \ rough 810 or (resid 811 and (name N or name CA or name C or name O or name CB )) \ or resid 812 through 813 or (resid 814 and (name N or name CA or name C or name \ O or name CB )) or resid 815 through 865 or (resid 866 through 868 and (name N \ or name CA or name C or name O or name CB )) or resid 869 through 920 or (resid \ 921 and (name N or name CA or name C or name O or name CB )) or resid 922 throug \ h 928 or (resid 929 through 931 and (name N or name CA or name C or name O or na \ me CB )) or resid 932 through 935 or (resid 936 through 937 and (name N or name \ CA or name C or name O or name CB )) or resid 938 through 941 or (resid 943 thro \ ugh 944 and (name N or name CA or name C or name O or name CB )) or resid 945 th \ rough 950 or (resid 951 and (name N or name CA or name C or name O or name CB )) \ or resid 952 through 963 or (resid 964 and (name N or name CA or name C or name \ O or name CB )) or resid 965 through 977 or (resid 978 through 979 and (name N \ or name CA or name C or name O or name CB )) or resid 980 through 982 or (resid \ 983 through 985 and (name N or name CA or name C or name O or name CB )) or resi \ d 986 through 993 or (resid 994 and (name N or name CA or name C or name O or na \ me CB )) or resid 995 through 1054 or (resid 1055 through 1056 and (name N or na \ me CA or name C or name O or name CB )) or resid 1057 through 1083 or (resid 108 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 1085 through \ 1096 or (resid 1097 and (name N or name CA or name C or name O or name CB )) or \ resid 1098 through 1115 or (resid 1116 and (name N or name CA or name C or name \ O or name CB )) or resid 1117 through 1135 or (resid 1136 and (name N or name C \ A or name C or name O or name CB )) or resid 1137 through 1501)) } ncs_group { reference = chain 'D' selection = (chain 'F' and (resid 2 through 29 or (resid 30 through 32 and (name N or name C \ A or name C or name O or name CB )) or resid 33 through 121)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'I' selection = (chain 'J' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 109)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.250 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 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 0.098 24315 Z= 0.272 Angle : 0.645 12.770 33424 Z= 0.377 Chirality : 0.051 0.420 4059 Planarity : 0.007 0.209 4338 Dihedral : 9.793 89.963 8395 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.93 % Rotamer: Outliers : 1.16 % Allowed : 5.37 % Favored : 93.47 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.14), residues: 3325 helix: -1.79 (0.17), residues: 680 sheet: 0.66 (0.19), residues: 813 loop : -0.66 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 634 TYR 0.023 0.001 TYR B 266 PHE 0.022 0.002 PHE C 92 TRP 0.013 0.001 TRP C 633 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00509 (24224) covalent geometry : angle 0.63326 (33193) SS BOND : bond 0.00232 ( 42) SS BOND : angle 0.99676 ( 84) hydrogen bonds : bond 0.26444 ( 1048) hydrogen bonds : angle 10.21464 ( 3009) link_BETA1-4 : bond 0.00311 ( 10) link_BETA1-4 : angle 1.29984 ( 30) link_NAG-ASN : bond 0.00401 ( 39) link_NAG-ASN : angle 1.93761 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 0.760 Fit side-chains REVERT: A 33 PHE cc_start: 0.7078 (m-80) cc_final: 0.6836 (m-80) REVERT: A 42 LYS cc_start: 0.7235 (mttt) cc_final: 0.6858 (mtmt) REVERT: A 269 TYR cc_start: 0.8187 (m-80) cc_final: 0.7648 (m-10) REVERT: A 307 THR cc_start: 0.8751 (m) cc_final: 0.8535 (p) REVERT: A 453 TYR cc_start: 0.6733 (p90) cc_final: 0.6382 (p90) REVERT: A 574 ASP cc_start: 0.7053 (t70) cc_final: 0.6763 (t0) REVERT: A 804 GLN cc_start: 0.8570 (mt0) cc_final: 0.8167 (mt0) REVERT: A 935 GLN cc_start: 0.7290 (mt0) cc_final: 0.6793 (mt0) REVERT: A 1010 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7838 (mp10) REVERT: B 170 TYR cc_start: 0.7146 (t80) cc_final: 0.6921 (t80) REVERT: B 195 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6624 (ttpp) REVERT: B 304 LYS cc_start: 0.7825 (mttt) cc_final: 0.7555 (mtpt) REVERT: B 537 LYS cc_start: 0.7322 (mttt) cc_final: 0.7066 (mmmm) REVERT: B 583 GLU cc_start: 0.8327 (pt0) cc_final: 0.8111 (pt0) REVERT: B 690 GLN cc_start: 0.6806 (mm-40) cc_final: 0.6595 (mm-40) REVERT: B 703 ASN cc_start: 0.7756 (t0) cc_final: 0.7185 (t0) REVERT: B 779 GLN cc_start: 0.7745 (tt0) cc_final: 0.7200 (tp40) REVERT: B 969 LYS cc_start: 0.8058 (mttt) cc_final: 0.7816 (mttm) REVERT: B 976 VAL cc_start: 0.7891 (t) cc_final: 0.7679 (m) REVERT: B 1010 GLN cc_start: 0.7897 (mt0) cc_final: 0.7289 (mm-40) REVERT: C 191 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8441 (mt-10) REVERT: C 294 ASP cc_start: 0.7202 (p0) cc_final: 0.7000 (p0) REVERT: C 307 THR cc_start: 0.8246 (m) cc_final: 0.8036 (p) REVERT: C 754 LEU cc_start: 0.8137 (mt) cc_final: 0.7832 (mp) REVERT: C 947 LYS cc_start: 0.8173 (mttt) cc_final: 0.7955 (mtmt) REVERT: C 983 ARG cc_start: 0.7718 (ttp-110) cc_final: 0.7395 (ttp-110) REVERT: C 1010 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.6516 (pt0) outliers start: 21 outliers final: 10 residues processed: 239 average time/residue: 0.1371 time to fit residues: 52.4809 Evaluate side-chains 168 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 197 optimal weight: 0.0030 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.0170 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.0370 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.2706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 613 GLN A1048 HIS B 271 GLN B1048 HIS C 67 HIS C1048 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.184230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.160576 restraints weight = 27437.793| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.17 r_work: 0.3496 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 24315 Z= 0.111 Angle : 0.530 8.392 33424 Z= 0.274 Chirality : 0.045 0.244 4059 Planarity : 0.004 0.036 4338 Dihedral : 4.668 59.086 4593 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.29 % Favored : 97.65 % Rotamer: Outliers : 1.55 % Allowed : 7.53 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.14), residues: 3325 helix: 0.19 (0.20), residues: 681 sheet: 0.64 (0.18), residues: 839 loop : -0.50 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.018 0.001 TYR C1067 PHE 0.017 0.001 PHE B 855 TRP 0.010 0.001 TRP A 65 HIS 0.003 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00233 (24224) covalent geometry : angle 0.50862 (33193) SS BOND : bond 0.00327 ( 42) SS BOND : angle 1.64120 ( 84) hydrogen bonds : bond 0.04637 ( 1048) hydrogen bonds : angle 6.27484 ( 3009) link_BETA1-4 : bond 0.00409 ( 10) link_BETA1-4 : angle 1.28211 ( 30) link_NAG-ASN : bond 0.00366 ( 39) link_NAG-ASN : angle 2.09552 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.852 Fit side-chains REVERT: A 33 PHE cc_start: 0.8267 (m-80) cc_final: 0.8049 (m-80) REVERT: A 453 TYR cc_start: 0.7851 (p90) cc_final: 0.7575 (p90) REVERT: A 739 THR cc_start: 0.9009 (m) cc_final: 0.8703 (p) REVERT: A 935 GLN cc_start: 0.7953 (mt0) cc_final: 0.7714 (tt0) REVERT: C 574 ASP cc_start: 0.8298 (m-30) cc_final: 0.7937 (m-30) REVERT: C 754 LEU cc_start: 0.9057 (mt) cc_final: 0.8837 (mp) REVERT: C 762 GLN cc_start: 0.8506 (mt0) cc_final: 0.8215 (mm-40) outliers start: 28 outliers final: 13 residues processed: 200 average time/residue: 0.1225 time to fit residues: 41.0980 Evaluate side-chains 158 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 87 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 292 optimal weight: 1.9990 chunk 290 optimal weight: 0.9990 chunk 119 optimal weight: 0.2980 chunk 49 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 323 optimal weight: 0.9980 chunk 187 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A 901 GLN A 965 GLN A1119 ASN B1010 GLN C 628 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.183025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.159939 restraints weight = 27476.368| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.15 r_work: 0.3475 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24315 Z= 0.134 Angle : 0.510 9.146 33424 Z= 0.259 Chirality : 0.045 0.226 4059 Planarity : 0.004 0.036 4338 Dihedral : 4.316 58.301 4582 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.65 % Favored : 97.32 % Rotamer: Outliers : 1.83 % Allowed : 8.42 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.15), residues: 3325 helix: 0.97 (0.21), residues: 680 sheet: 0.69 (0.18), residues: 842 loop : -0.52 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.021 0.001 TYR B1067 PHE 0.015 0.001 PHE C1121 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00319 (24224) covalent geometry : angle 0.49065 (33193) SS BOND : bond 0.00317 ( 42) SS BOND : angle 1.37860 ( 84) hydrogen bonds : bond 0.04242 ( 1048) hydrogen bonds : angle 5.66656 ( 3009) link_BETA1-4 : bond 0.00368 ( 10) link_BETA1-4 : angle 1.24265 ( 30) link_NAG-ASN : bond 0.00246 ( 39) link_NAG-ASN : angle 2.03240 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.865 Fit side-chains REVERT: A 269 TYR cc_start: 0.8652 (m-80) cc_final: 0.8438 (m-10) REVERT: A 453 TYR cc_start: 0.7995 (p90) cc_final: 0.7739 (p90) REVERT: B 869 MET cc_start: 0.8826 (mtp) cc_final: 0.8557 (mtp) REVERT: C 918 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8328 (mm-30) outliers start: 33 outliers final: 28 residues processed: 174 average time/residue: 0.1199 time to fit residues: 35.1973 Evaluate side-chains 159 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 58 optimal weight: 0.8980 chunk 15 optimal weight: 50.0000 chunk 270 optimal weight: 50.0000 chunk 207 optimal weight: 0.0770 chunk 129 optimal weight: 0.6980 chunk 193 optimal weight: 0.4980 chunk 210 optimal weight: 1.9990 chunk 273 optimal weight: 50.0000 chunk 241 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN B1010 GLN C1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.191429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.156875 restraints weight = 27783.735| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.64 r_work: 0.3478 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24315 Z= 0.151 Angle : 0.513 7.733 33424 Z= 0.259 Chirality : 0.045 0.219 4059 Planarity : 0.004 0.037 4338 Dihedral : 4.309 59.479 4582 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 2.33 % Allowed : 9.36 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.15), residues: 3325 helix: 1.23 (0.21), residues: 669 sheet: 0.65 (0.18), residues: 856 loop : -0.55 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 567 TYR 0.021 0.001 TYR B1067 PHE 0.015 0.001 PHE B 92 TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00367 (24224) covalent geometry : angle 0.49492 (33193) SS BOND : bond 0.00334 ( 42) SS BOND : angle 1.30847 ( 84) hydrogen bonds : bond 0.03982 ( 1048) hydrogen bonds : angle 5.32564 ( 3009) link_BETA1-4 : bond 0.00351 ( 10) link_BETA1-4 : angle 1.24165 ( 30) link_NAG-ASN : bond 0.00329 ( 39) link_NAG-ASN : angle 1.99642 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.7727 (p90) cc_final: 0.7456 (p90) outliers start: 42 outliers final: 29 residues processed: 173 average time/residue: 0.1029 time to fit residues: 30.9828 Evaluate side-chains 163 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 223 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 chunk 295 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 chunk 332 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 12 optimal weight: 50.0000 chunk 137 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 39 optimal weight: 40.0000 chunk 282 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1010 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.190473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.156261 restraints weight = 27684.171| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 1.60 r_work: 0.3479 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24315 Z= 0.190 Angle : 0.540 7.380 33424 Z= 0.272 Chirality : 0.046 0.219 4059 Planarity : 0.004 0.042 4338 Dihedral : 4.477 59.583 4582 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer: Outliers : 2.88 % Allowed : 9.52 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.15), residues: 3325 helix: 1.23 (0.21), residues: 675 sheet: 0.68 (0.18), residues: 855 loop : -0.56 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.022 0.001 TYR B1067 PHE 0.017 0.002 PHE C1121 TRP 0.009 0.001 TRP A 436 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00466 (24224) covalent geometry : angle 0.51981 (33193) SS BOND : bond 0.00411 ( 42) SS BOND : angle 1.46140 ( 84) hydrogen bonds : bond 0.04142 ( 1048) hydrogen bonds : angle 5.27404 ( 3009) link_BETA1-4 : bond 0.00305 ( 10) link_BETA1-4 : angle 1.29368 ( 30) link_NAG-ASN : bond 0.00377 ( 39) link_NAG-ASN : angle 2.15500 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 134 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6921 (OUTLIER) cc_final: 0.6675 (p90) REVERT: A 453 TYR cc_start: 0.7658 (p90) cc_final: 0.7408 (p90) REVERT: B 740 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8614 (ttt) REVERT: C 787 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8353 (mt0) REVERT: C 905 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8715 (mtt90) outliers start: 52 outliers final: 38 residues processed: 174 average time/residue: 0.1216 time to fit residues: 36.2164 Evaluate side-chains 175 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 905 ARG Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.797 > 50: distance: 9 - 165: 21.150 distance: 12 - 162: 15.027 distance: 53 - 190: 8.215 distance: 56 - 187: 4.845 distance: 65 - 176: 10.069 distance: 68 - 173: 6.681 distance: 81 - 160: 12.171 distance: 84 - 157: 28.132 distance: 111 - 195: 8.736 distance: 129 - 131: 7.105 distance: 131 - 132: 15.026 distance: 132 - 133: 20.642 distance: 132 - 135: 13.205 distance: 133 - 134: 23.550 distance: 133 - 139: 27.280 distance: 135 - 136: 18.566 distance: 135 - 137: 13.264 distance: 136 - 138: 14.461 distance: 139 - 140: 3.153 distance: 140 - 141: 7.662 distance: 140 - 143: 10.401 distance: 141 - 142: 11.809 distance: 141 - 147: 8.815 distance: 143 - 144: 5.491 distance: 144 - 145: 18.491 distance: 144 - 146: 12.979 distance: 146 - 209: 28.171 distance: 147 - 148: 12.497 distance: 148 - 149: 14.750 distance: 148 - 151: 12.803 distance: 149 - 150: 8.642 distance: 149 - 152: 5.853 distance: 152 - 153: 8.020 distance: 153 - 156: 11.117 distance: 154 - 155: 9.917 distance: 154 - 157: 14.004 distance: 157 - 158: 15.695 distance: 158 - 159: 7.266 distance: 158 - 161: 12.202 distance: 159 - 160: 10.301 distance: 159 - 162: 8.164 distance: 162 - 163: 5.339 distance: 163 - 166: 9.234 distance: 164 - 165: 10.375 distance: 164 - 173: 8.704 distance: 166 - 167: 8.207 distance: 167 - 168: 9.673 distance: 167 - 169: 6.478 distance: 168 - 170: 9.568 distance: 169 - 171: 8.835 distance: 170 - 172: 5.824 distance: 171 - 172: 11.727 distance: 173 - 174: 4.724 distance: 174 - 175: 6.081 distance: 174 - 177: 4.512 distance: 175 - 176: 6.374 distance: 175 - 182: 3.896 distance: 177 - 178: 9.476 distance: 178 - 179: 6.527 distance: 179 - 181: 14.303 distance: 182 - 183: 3.452 distance: 183 - 184: 4.323 distance: 183 - 186: 9.318 distance: 184 - 185: 4.107 distance: 187 - 188: 4.054 distance: 188 - 189: 11.702 distance: 188 - 191: 12.053 distance: 189 - 192: 5.499 distance: 192 - 193: 5.920 distance: 193 - 196: 4.557 distance: 194 - 197: 7.093