Starting phenix.real_space_refine on Tue May 27 10:52:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mxd_24071/05_2025/7mxd_24071.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mxd_24071/05_2025/7mxd_24071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mxd_24071/05_2025/7mxd_24071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mxd_24071/05_2025/7mxd_24071.map" model { file = "/net/cci-nas-00/data/ceres_data/7mxd_24071/05_2025/7mxd_24071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mxd_24071/05_2025/7mxd_24071.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 145 5.16 5 C 18502 2.51 5 N 4835 2.21 5 O 6011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29496 Number of models: 1 Model: "" Number of chains: 58 Chain: "A" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3731 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 24, 'TRANS': 447} Chain: "C" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1676 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "D" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1603 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Chain: "F" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3731 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 24, 'TRANS': 447} Chain: "G" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3731 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 24, 'TRANS': 447} Chain: "J" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1676 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "K" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1603 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Chain: "S" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1676 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "U" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1603 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Chain: "X" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1653 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "Y" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1631 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "B" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain breaks: 1 Chain: "I" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain breaks: 1 Chain: "H" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain breaks: 1 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: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" 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: "V" 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: "W" 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: "Z" 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: 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: "b" 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: "c" 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: "d" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "e" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "f" 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: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "p" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" 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: "t" 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: "u" 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: "v" 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: "w" 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: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 117 Unusual residues: {'NAG': 8, 'PO4': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 122 Unusual residues: {'NAG': 8, 'PO4': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 17.34, per 1000 atoms: 0.59 Number of scatterers: 29496 At special positions: 0 Unit cell: (174.08, 172.72, 171.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 145 16.00 P 3 15.00 O 6011 8.00 N 4835 7.00 C 18502 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=53, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.05 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.04 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS H 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 140 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS S 140 " - pdb=" SG CYS S 196 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.04 Simple disulfide: pdb=" SG CYS U 134 " - pdb=" SG CYS U 194 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.03 Simple disulfide: pdb=" SG CYS X 139 " - pdb=" SG CYS Y 214 " distance=2.03 Simple disulfide: pdb=" SG CYS X 152 " - pdb=" SG CYS X 208 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 134 " - pdb=" SG CYS Y 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 598 " - pdb=" SG CYS H 604 " 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 ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN d 4 " - " MAN d 5 " " MAN o 4 " - " MAN o 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " MAN N 7 " - " MAN N 8 " " BMA O 3 " - " MAN O 7 " " MAN O 4 " - " MAN O 5 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 7 " " MAN e 4 " - " MAN e 5 " " BMA m 3 " - " MAN m 7 " " MAN m 4 " - " MAN m 5 " " BMA o 3 " - " MAN o 4 " " BMA p 3 " - " MAN p 7 " " MAN p 4 " - " MAN p 5 " ALPHA1-6 " BMA N 3 " - " MAN N 7 " " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 6 " " BMA d 3 " - " MAN d 6 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 6 " " BMA m 3 " - " MAN m 4 " " MAN m 4 " - " MAN m 6 " " BMA o 3 " - " MAN o 6 " " BMA p 3 " - " MAN p 4 " " MAN p 4 " - " MAN p 6 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 392 " " NAG A 605 " - " ASN A 149 " " NAG A 606 " - " ASN A 355 " " NAG A 607 " - " ASN A 405 " " NAG A 608 " - " ASN A 339 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 616 " " NAG D 301 " - " ASN D 72 " " NAG E 1 " - " ASN A 156 " " NAG F 603 " - " ASN F 133 " " NAG F 604 " - " ASN F 234 " " NAG F 605 " - " ASN F 301 " " NAG F 606 " - " ASN F 392 " " NAG F 607 " - " ASN F 149 " " NAG F 608 " - " ASN F 355 " " NAG F 609 " - " ASN F 405 " " NAG F 610 " - " ASN F 339 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 160 " " NAG G 603 " - " ASN G 197 " " NAG G 604 " - " ASN G 234 " " NAG G 605 " - " ASN G 301 " " NAG G 606 " - " ASN G 392 " " NAG G 607 " - " ASN G 149 " " NAG G 608 " - " ASN G 355 " " NAG G 609 " - " ASN G 339 " " NAG H 701 " - " ASN H 611 " " NAG H 702 " - " ASN H 637 " " NAG H 703 " - " ASN H 625 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 637 " " NAG I 703 " - " ASN I 616 " " NAG K 301 " - " ASN K 72 " " NAG L 1 " - " ASN A 160 " " NAG M 1 " - " ASN A 197 " " NAG N 1 " - " ASN A 262 " " NAG O 1 " - " ASN A 276 " " NAG P 1 " - " ASN A 295 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 448 " " NAG T 1 " - " ASN A 88 " " NAG U 301 " - " ASN U 72 " " NAG V 1 " - " ASN A 334 " " NAG W 1 " - " ASN A 241 " " NAG Z 1 " - " ASN A 289 " " NAG a 1 " - " ASN I 625 " " NAG b 1 " - " ASN F 156 " " NAG c 1 " - " ASN F 197 " " NAG d 1 " - " ASN F 262 " " NAG e 1 " - " ASN F 276 " " NAG f 1 " - " ASN F 295 " " NAG g 1 " - " ASN F 386 " " NAG h 1 " - " ASN F 448 " " NAG i 1 " - " ASN F 88 " " NAG j 1 " - " ASN F 334 " " NAG k 1 " - " ASN F 241 " " NAG l 1 " - " ASN F 289 " " NAG m 1 " - " ASN F 160 " " NAG n 1 " - " ASN G 156 " " NAG o 1 " - " ASN G 262 " " NAG p 1 " - " ASN G 276 " " NAG q 1 " - " ASN G 295 " " NAG r 1 " - " ASN G 386 " " NAG s 1 " - " ASN G 448 " " NAG t 1 " - " ASN G 88 " " NAG u 1 " - " ASN G 334 " " NAG v 1 " - " ASN G 241 " " NAG w 1 " - " ASN G 289 " Time building additional restraints: 9.22 Conformation dependent library (CDL) restraints added in 3.3 seconds 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6576 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 78 sheets defined 14.9% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.11 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.221A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.573A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 removed outlier: 4.233A pdb=" N GLU A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.560A pdb=" N ASP A 477 " --> pdb=" O ASN A 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.607A pdb=" N ASP C 31 " --> pdb=" O ASN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.521A pdb=" N ASP C 86 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 83 through 87' Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.716A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.552A pdb=" N LEU D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 121 through 126' Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.390A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 126 Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'F' and resid 335 through 353 removed outlier: 3.712A pdb=" N LYS F 343 " --> pdb=" O ASN F 339 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU F 351 " --> pdb=" O GLY F 347 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS F 352 " --> pdb=" O LYS F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 474 through 479 removed outlier: 3.605A pdb=" N ASP F 477 " --> pdb=" O ASN F 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.520A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 353 removed outlier: 3.986A pdb=" N GLU G 351 " --> pdb=" O GLY G 347 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.619A pdb=" N MET G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.608A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.662A pdb=" N ASP J 31 " --> pdb=" O ASN J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.820A pdb=" N ASP J 86 " --> pdb=" O ARG J 83 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR J 87 " --> pdb=" O SER J 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 83 through 87' Processing helix chain 'J' and resid 185 through 189 Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.011A pdb=" N ILE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 126 removed outlier: 3.766A pdb=" N LEU K 125 " --> pdb=" O SER K 121 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 121 through 126' Processing helix chain 'K' and resid 182 through 189 removed outlier: 3.588A pdb=" N HIS K 189 " --> pdb=" O ASP K 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.559A pdb=" N ASP S 31 " --> pdb=" O ASN S 28 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR S 32 " --> pdb=" O ILE S 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 28 through 32' Processing helix chain 'S' and resid 83 through 87 removed outlier: 3.921A pdb=" N THR S 87 " --> pdb=" O SER S 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 83 removed outlier: 3.903A pdb=" N ILE U 83 " --> pdb=" O PRO U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 121 through 126 removed outlier: 3.749A pdb=" N LEU U 125 " --> pdb=" O SER U 121 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS U 126 " --> pdb=" O ASP U 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 121 through 126' Processing helix chain 'U' and resid 182 through 189 removed outlier: 3.635A pdb=" N TYR U 186 " --> pdb=" O SER U 182 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU U 187 " --> pdb=" O LYS U 183 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS U 188 " --> pdb=" O ALA U 184 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HIS U 189 " --> pdb=" O ASP U 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 182 through 189' Processing helix chain 'X' and resid 61 through 65 Processing helix chain 'Y' and resid 121 through 125 Processing helix chain 'Y' and resid 182 through 187 removed outlier: 3.838A pdb=" N GLN Y 187 " --> pdb=" O ASN Y 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 535 removed outlier: 3.896A pdb=" N ASN B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 532 through 535' Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.929A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 568 Processing helix chain 'B' and resid 569 through 574 removed outlier: 3.517A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 597 removed outlier: 4.098A pdb=" N VAL B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 659 removed outlier: 3.952A pdb=" N ASP B 644 " --> pdb=" O SER B 640 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 542 removed outlier: 4.014A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 547 through 551 removed outlier: 4.028A pdb=" N GLN I 550 " --> pdb=" O GLY I 547 " (cutoff:3.500A) Processing helix chain 'I' and resid 565 through 568 Processing helix chain 'I' and resid 569 through 597 removed outlier: 3.606A pdb=" N LYS I 574 " --> pdb=" O VAL I 570 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN I 575 " --> pdb=" O TRP I 571 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU I 576 " --> pdb=" O GLY I 572 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL I 589 " --> pdb=" O ARG I 585 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE I 592 " --> pdb=" O GLU I 588 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 625 removed outlier: 3.943A pdb=" N ASN I 625 " --> pdb=" O GLN I 621 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 659 removed outlier: 4.069A pdb=" N ASP I 644 " --> pdb=" O SER I 640 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN I 650 " --> pdb=" O LEU I 646 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP I 659 " --> pdb=" O ILE I 655 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 534 Processing helix chain 'H' and resid 547 through 551 removed outlier: 3.759A pdb=" N GLN H 550 " --> pdb=" O GLY H 547 " (cutoff:3.500A) Processing helix chain 'H' and resid 565 through 568 Processing helix chain 'H' and resid 569 through 597 removed outlier: 3.611A pdb=" N LYS H 574 " --> pdb=" O VAL H 570 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN H 575 " --> pdb=" O TRP H 571 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU H 576 " --> pdb=" O GLY H 572 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA H 582 " --> pdb=" O ALA H 578 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL H 589 " --> pdb=" O ARG H 585 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE H 592 " --> pdb=" O GLU H 588 " (cutoff:3.500A) Processing helix chain 'H' and resid 619 through 624 Processing helix chain 'H' and resid 627 through 635 Processing helix chain 'H' and resid 638 through 659 removed outlier: 4.071A pdb=" N ASP H 644 " --> pdb=" O SER H 640 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.148A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 132 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.859A pdb=" N LYS A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 284 through 312 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 271 through 274 current: chain 'A' and resid 441 through 456 Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.614A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 414 through 421 removed outlier: 4.555A pdb=" N ASN A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU A 293 " --> pdb=" O ASN A 334 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.956A pdb=" N LYS A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.747A pdb=" N ASN A 448 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 10.773A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 10.054A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.408A pdb=" N ILE A 294 " --> pdb=" O ASN A 444 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N ASN A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.193A pdb=" N CYS A 296 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N LYS A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 393 through 395 removed outlier: 3.737A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.218A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 358 through 361 removed outlier: 6.282A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AB6, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.612A pdb=" N ALA C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.612A pdb=" N ALA C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 124 removed outlier: 4.179A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 120 through 124 removed outlier: 4.179A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.542A pdb=" N ASP D 105 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AC5, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.566A pdb=" N TYR D 49 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 116 through 118 removed outlier: 3.601A pdb=" N LEU D 135 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE D 118 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL D 133 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU D 179 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU D 135 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N SER D 177 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASN D 137 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU D 175 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 145 through 146 removed outlier: 4.234A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR D 197 " --> pdb=" O LYS D 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.005A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AD1, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.623A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AD3, first strand: chain 'F' and resid 120 through 121 removed outlier: 3.822A pdb=" N VAL F 120 " --> pdb=" O GLN F 203 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 130 through 132 removed outlier: 3.539A pdb=" N GLY X 106 " --> pdb=" O ASP X 103 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 181 through 183 Processing sheet with id=AD6, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.216A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLY F 441 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N SER F 300 " --> pdb=" O GLY F 441 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY F 451 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N LYS F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 11.874A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 11.780A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 10.810A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.164A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 284 through 302 current: chain 'F' and resid 358 through 361 Processing sheet with id=AD7, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.164A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.810A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.780A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 11.874A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N LYS F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY F 451 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N SER F 300 " --> pdb=" O GLY F 441 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLY F 441 " --> pdb=" O SER F 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 441 through 456 current: chain 'F' and resid 414 through 421 removed outlier: 4.220A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 305 through 309 removed outlier: 3.729A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 494 through 499 Processing sheet with id=AE1, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AE2, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AE3, first strand: chain 'G' and resid 91 through 93 Processing sheet with id=AE4, first strand: chain 'G' and resid 154 through 162 Processing sheet with id=AE5, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AE6, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.711A pdb=" N LYS G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.224A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.224A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 315 through 322 removed outlier: 6.750A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 315 through 322 removed outlier: 6.750A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N SER G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLY G 441 " --> pdb=" O SER G 300 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.734A pdb=" N VAL J 18 " --> pdb=" O LEU J 82 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.515A pdb=" N ALA J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TRP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.515A pdb=" N ALA J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 120 through 123 removed outlier: 6.208A pdb=" N TYR J 176 " --> pdb=" O ASP J 144 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL J 181 " --> pdb=" O HIS J 164 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 120 through 123 removed outlier: 6.208A pdb=" N TYR J 176 " --> pdb=" O ASP J 144 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 151 through 154 removed outlier: 3.558A pdb=" N THR J 151 " --> pdb=" O ASN J 199 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL J 207 " --> pdb=" O VAL J 198 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 18 through 24 Processing sheet with id=AF9, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.403A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 114 through 118 removed outlier: 4.005A pdb=" N ASN K 137 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL K 133 " --> pdb=" O PHE K 118 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 149 through 150 Processing sheet with id=AG3, first strand: chain 'S' and resid 5 through 6 removed outlier: 3.974A pdb=" N VAL S 18 " --> pdb=" O LEU S 82 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 5 through 6 Processing sheet with id=AG5, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.304A pdb=" N ALA S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.304A pdb=" N ALA S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL S 102 " --> pdb=" O ARG S 94 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'S' and resid 120 through 123 removed outlier: 5.825A pdb=" N TYR S 176 " --> pdb=" O ASP S 144 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL S 181 " --> pdb=" O HIS S 164 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'S' and resid 120 through 123 removed outlier: 5.825A pdb=" N TYR S 176 " --> pdb=" O ASP S 144 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 151 through 154 removed outlier: 3.722A pdb=" N THR S 151 " --> pdb=" O ASN S 199 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR S 194 " --> pdb=" O VAL S 211 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'U' and resid 11 through 12 removed outlier: 3.580A pdb=" N LEU U 11 " --> pdb=" O ARG U 103 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP U 105 " --> pdb=" O LEU U 11 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR U 86 " --> pdb=" O THR U 102 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP U 35 " --> pdb=" O LEU U 47 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'U' and resid 19 through 24 Processing sheet with id=AH3, first strand: chain 'U' and resid 114 through 118 removed outlier: 3.551A pdb=" N PHE U 118 " --> pdb=" O VAL U 133 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL U 133 " --> pdb=" O PHE U 118 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER U 177 " --> pdb=" O CYS U 134 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR U 173 " --> pdb=" O ASN U 138 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'U' and resid 145 through 146 removed outlier: 4.238A pdb=" N LYS U 145 " --> pdb=" O THR U 197 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR U 197 " --> pdb=" O LYS U 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'X' and resid 3 through 6 removed outlier: 3.514A pdb=" N ILE X 79 " --> pdb=" O CYS X 22 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'X' and resid 45 through 51 removed outlier: 4.077A pdb=" N TRP X 36 " --> pdb=" O ILE X 48 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ARG X 50 " --> pdb=" O CYS X 34 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N CYS X 34 " --> pdb=" O ARG X 50 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE X 37 " --> pdb=" O PHE X 95 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N GLY X 98 " --> pdb=" O LYS X 113 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS X 113 " --> pdb=" O GLY X 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'X' and resid 92 through 93 Processing sheet with id=AH8, first strand: chain 'X' and resid 132 through 136 removed outlier: 3.764A pdb=" N GLY X 151 " --> pdb=" O LEU X 136 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N TYR X 188 " --> pdb=" O ASP X 156 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 132 through 136 removed outlier: 3.764A pdb=" N GLY X 151 " --> pdb=" O LEU X 136 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA X 148 " --> pdb=" O VAL X 196 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL X 196 " --> pdb=" O ALA X 148 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU X 150 " --> pdb=" O VAL X 194 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL X 194 " --> pdb=" O LEU X 150 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'X' and resid 162 through 166 removed outlier: 3.632A pdb=" N SER X 165 " --> pdb=" O ASN X 209 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 4 through 7 removed outlier: 3.583A pdb=" N VAL Y 19 " --> pdb=" O ILE Y 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE Y 71 " --> pdb=" O CYS Y 23 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Y' and resid 11 through 12 removed outlier: 7.162A pdb=" N VAL Y 11 " --> pdb=" O GLU Y 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'Y' and resid 53 through 54 removed outlier: 3.657A pdb=" N LYS Y 45 " --> pdb=" O GLN Y 37 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP Y 35 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR Y 85 " --> pdb=" O ALA Y 38 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Y' and resid 114 through 115 removed outlier: 4.050A pdb=" N VAL Y 132 " --> pdb=" O LEU Y 179 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Y' and resid 146 through 148 915 hydrogen bonds defined for protein. 2307 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: 10.57 Time building geometry restraints manager: 10.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9182 1.35 - 1.47: 7883 1.47 - 1.60: 12890 1.60 - 1.72: 0 1.72 - 1.85: 183 Bond restraints: 30138 Sorted by residual: bond pdb=" O3 PO4 F 602 " pdb=" P PO4 F 602 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.11e+00 bond pdb=" O3 PO4 F 601 " pdb=" P PO4 F 601 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.11e+00 bond pdb=" O3 PO4 A 609 " pdb=" P PO4 A 609 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" O4 PO4 F 601 " pdb=" P PO4 F 601 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 8.91e+00 bond pdb=" O4 PO4 F 602 " pdb=" P PO4 F 602 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.71e+00 ... (remaining 30133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 39537 1.75 - 3.51: 1257 3.51 - 5.26: 162 5.26 - 7.02: 56 7.02 - 8.77: 11 Bond angle restraints: 41023 Sorted by residual: angle pdb=" N ASN F 156 " pdb=" CA ASN F 156 " pdb=" CB ASN F 156 " ideal model delta sigma weight residual 109.85 118.61 -8.76 1.49e+00 4.50e-01 3.45e+01 angle pdb=" N ASN I 625 " pdb=" CA ASN I 625 " pdb=" CB ASN I 625 " ideal model delta sigma weight residual 111.54 119.51 -7.97 1.45e+00 4.76e-01 3.02e+01 angle pdb=" C ASN I 625 " pdb=" CA ASN I 625 " pdb=" CB ASN I 625 " ideal model delta sigma weight residual 111.18 103.02 8.16 1.56e+00 4.11e-01 2.74e+01 angle pdb=" C ASN I 624 " pdb=" N ASN I 625 " pdb=" CA ASN I 625 " ideal model delta sigma weight residual 122.50 113.73 8.77 1.82e+00 3.02e-01 2.32e+01 angle pdb=" C LYS D 107 " pdb=" N ARG D 108 " pdb=" CA ARG D 108 " ideal model delta sigma weight residual 121.54 128.55 -7.01 1.91e+00 2.74e-01 1.35e+01 ... (remaining 41018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 18533 24.42 - 48.84: 979 48.84 - 73.26: 215 73.26 - 97.67: 103 97.67 - 122.09: 31 Dihedral angle restraints: 19861 sinusoidal: 9652 harmonic: 10209 Sorted by residual: dihedral pdb=" CB CYS U 134 " pdb=" SG CYS U 134 " pdb=" SG CYS U 194 " pdb=" CB CYS U 194 " ideal model delta sinusoidal sigma weight residual -86.00 3.48 -89.48 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS F 501 " pdb=" SG CYS F 501 " pdb=" SG CYS I 605 " pdb=" CB CYS I 605 " ideal model delta sinusoidal sigma weight residual 93.00 4.13 88.87 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS G 126 " pdb=" SG CYS G 126 " pdb=" SG CYS G 196 " pdb=" CB CYS G 196 " ideal model delta sinusoidal sigma weight residual -86.00 -173.74 87.74 1 1.00e+01 1.00e-02 9.22e+01 ... (remaining 19858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.253: 5007 0.253 - 0.506: 14 0.506 - 0.759: 1 0.759 - 1.012: 0 1.012 - 1.265: 2 Chirality restraints: 5024 Sorted by residual: chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN F 156 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.14 -1.26 2.00e-01 2.50e+01 4.00e+01 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN I 625 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.14 -1.26 2.00e-01 2.50e+01 3.99e+01 chirality pdb=" C1 NAG I 701 " pdb=" ND2 ASN I 611 " pdb=" C2 NAG I 701 " pdb=" O5 NAG I 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.15e+00 ... (remaining 5021 not shown) Planarity restraints: 5115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 156 " 0.069 2.00e-02 2.50e+03 6.67e-02 5.57e+01 pdb=" CG ASN F 156 " -0.081 2.00e-02 2.50e+03 pdb=" OD1 ASN F 156 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN F 156 " -0.077 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 625 " 0.006 2.00e-02 2.50e+03 6.42e-02 5.16e+01 pdb=" CG ASN I 625 " -0.071 2.00e-02 2.50e+03 pdb=" OD1 ASN I 625 " 0.075 2.00e-02 2.50e+03 pdb=" ND2 ASN I 625 " -0.076 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 392 " 0.039 2.00e-02 2.50e+03 3.57e-02 1.59e+01 pdb=" CG ASN A 392 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 392 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 392 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG A 604 " 0.038 2.00e-02 2.50e+03 ... (remaining 5112 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 584 2.67 - 3.22: 27157 3.22 - 3.78: 41957 3.78 - 4.34: 59437 4.34 - 4.90: 97531 Nonbonded interactions: 226666 Sorted by model distance: nonbonded pdb=" OD1 ASN A 386 " pdb=" OG1 THR A 388 " model vdw 2.107 3.040 nonbonded pdb=" OG SER U 63 " pdb=" OG1 THR U 74 " model vdw 2.158 3.040 nonbonded pdb=" ND2 ASN F 67 " pdb=" O ASP F 211 " model vdw 2.175 3.120 nonbonded pdb=" O TYR Y 186 " pdb=" OH TYR Y 192 " model vdw 2.181 3.040 nonbonded pdb=" OG SER D 63 " pdb=" OG1 THR D 74 " model vdw 2.184 3.040 ... (remaining 226661 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 31 through 507 or resid 603 through 608)) selection = (chain 'F' and (resid 31 through 507 or resid 603 through 608)) selection = (chain 'G' and (resid 31 through 507 or resid 603 through 608)) } ncs_group { reference = (chain 'B' and (resid 519 through 661 or resid 701 through 703)) selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'S' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'U' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' } ncs_group { reference = (chain 'N' and (resid 2 or resid 5 through 8)) selection = (chain 'O' and (resid 1 or resid 4 through 7)) selection = (chain 'e' and (resid 1 or resid 4 through 7)) selection = (chain 'm' and (resid 1 or resid 4 through 7)) selection = (chain 'p' and (resid 1 or resid 4 through 7)) } ncs_group { reference = chain 'd' selection = chain 'o' } 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 64.910 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 0.060 30334 Z= 0.238 Angle : 0.808 21.459 41558 Z= 0.367 Chirality : 0.057 1.265 5024 Planarity : 0.004 0.058 5042 Dihedral : 16.457 122.093 13126 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.14), residues: 3477 helix: -1.65 (0.23), residues: 422 sheet: -0.21 (0.16), residues: 1093 loop : -1.46 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP I 610 HIS 0.004 0.001 HIS F 287 PHE 0.013 0.001 PHE G 53 TYR 0.015 0.001 TYR H 638 ARG 0.006 0.000 ARG F 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00621 ( 73) link_NAG-ASN : angle 4.62938 ( 219) link_ALPHA1-6 : bond 0.00343 ( 11) link_ALPHA1-6 : angle 1.76425 ( 33) link_BETA1-4 : bond 0.00705 ( 43) link_BETA1-4 : angle 1.60871 ( 129) link_ALPHA1-2 : bond 0.00137 ( 4) link_ALPHA1-2 : angle 2.01865 ( 12) link_ALPHA1-3 : bond 0.00442 ( 12) link_ALPHA1-3 : angle 1.78244 ( 36) hydrogen bonds : bond 0.21207 ( 830) hydrogen bonds : angle 7.68045 ( 2307) SS BOND : bond 0.00472 ( 53) SS BOND : angle 2.03027 ( 106) covalent geometry : bond 0.00504 (30138) covalent geometry : angle 0.72174 (41023) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 3.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7607 (m-30) cc_final: 0.7115 (m-30) REVERT: C 28 ASN cc_start: 0.6854 (t0) cc_final: 0.6585 (t0) REVERT: C 72 ASP cc_start: 0.8449 (p0) cc_final: 0.7691 (p0) REVERT: C 145 TYR cc_start: 0.6239 (p90) cc_final: 0.6005 (p90) REVERT: D 26 ASN cc_start: 0.8538 (p0) cc_final: 0.8294 (p0) REVERT: D 70 GLU cc_start: 0.7812 (pt0) cc_final: 0.7596 (pt0) REVERT: F 213 ILE cc_start: 0.8972 (mt) cc_final: 0.8654 (tt) REVERT: K 36 TYR cc_start: 0.8729 (m-80) cc_final: 0.8489 (m-80) REVERT: S 19 ARG cc_start: 0.7865 (ttm170) cc_final: 0.7557 (ttm170) REVERT: X 23 ASP cc_start: 0.7618 (m-30) cc_final: 0.7025 (m-30) REVERT: X 155 LYS cc_start: 0.7533 (mmmm) cc_final: 0.7296 (mmtt) REVERT: H 620 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7471 (tm-30) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.4632 time to fit residues: 249.3903 Evaluate side-chains 281 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 292 optimal weight: 9.9990 chunk 262 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 314 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN F 229 ASN G 66 HIS ** G 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 204 ASN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.156247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.122618 restraints weight = 44927.883| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 4.21 r_work: 0.3027 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30334 Z= 0.165 Angle : 0.685 13.193 41558 Z= 0.330 Chirality : 0.048 0.566 5024 Planarity : 0.005 0.069 5042 Dihedral : 12.348 118.400 6696 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.64 % Allowed : 6.83 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3477 helix: -0.47 (0.26), residues: 410 sheet: -0.09 (0.16), residues: 1095 loop : -1.37 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 610 HIS 0.005 0.001 HIS G 287 PHE 0.014 0.001 PHE G 53 TYR 0.017 0.001 TYR D 173 ARG 0.007 0.000 ARG Y 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00537 ( 73) link_NAG-ASN : angle 3.56595 ( 219) link_ALPHA1-6 : bond 0.00522 ( 11) link_ALPHA1-6 : angle 1.91584 ( 33) link_BETA1-4 : bond 0.00510 ( 43) link_BETA1-4 : angle 1.49492 ( 129) link_ALPHA1-2 : bond 0.00231 ( 4) link_ALPHA1-2 : angle 1.85461 ( 12) link_ALPHA1-3 : bond 0.00885 ( 12) link_ALPHA1-3 : angle 2.03446 ( 36) hydrogen bonds : bond 0.05406 ( 830) hydrogen bonds : angle 5.77749 ( 2307) SS BOND : bond 0.00527 ( 53) SS BOND : angle 1.24470 ( 106) covalent geometry : bond 0.00378 (30138) covalent geometry : angle 0.62313 (41023) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 310 time to evaluate : 3.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8509 (m-30) cc_final: 0.8021 (m-30) REVERT: C 145 TYR cc_start: 0.6666 (p90) cc_final: 0.6301 (p90) REVERT: D 3 GLN cc_start: 0.8198 (pm20) cc_final: 0.7923 (pm20) REVERT: D 26 ASN cc_start: 0.8831 (p0) cc_final: 0.8333 (p0) REVERT: D 70 GLU cc_start: 0.8205 (pt0) cc_final: 0.7846 (pt0) REVERT: F 213 ILE cc_start: 0.9150 (mt) cc_final: 0.8827 (tt) REVERT: G 86 MET cc_start: 0.8341 (mtp) cc_final: 0.8101 (mtm) REVERT: K 82 ASP cc_start: 0.6427 (m-30) cc_final: 0.5973 (m-30) REVERT: K 106 LEU cc_start: 0.6900 (mp) cc_final: 0.6667 (mp) REVERT: S 13 LYS cc_start: 0.8693 (tttm) cc_final: 0.8184 (mptt) REVERT: S 19 ARG cc_start: 0.7995 (ttm170) cc_final: 0.7558 (ttm170) REVERT: S 28 ASN cc_start: 0.7843 (t0) cc_final: 0.7575 (t0) REVERT: S 98 ASP cc_start: 0.8696 (m-30) cc_final: 0.8269 (t0) REVERT: U 61 ARG cc_start: 0.7260 (mtm110) cc_final: 0.6851 (mtm110) REVERT: U 77 ASN cc_start: 0.6073 (p0) cc_final: 0.5804 (p0) REVERT: H 620 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8104 (tm-30) outliers start: 20 outliers final: 14 residues processed: 319 average time/residue: 0.4780 time to fit residues: 232.4234 Evaluate side-chains 286 residues out of total 3106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 272 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain H residue 519 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.3414 > 50: distance: 62 - 67: 11.541 distance: 67 - 68: 19.948 distance: 68 - 69: 3.933 distance: 68 - 71: 15.451 distance: 69 - 70: 22.929 distance: 71 - 72: 3.497 distance: 72 - 73: 7.057 distance: 72 - 74: 5.020 distance: 73 - 75: 4.214 distance: 74 - 76: 4.258 distance: 75 - 76: 4.794 distance: 77 - 78: 38.980 distance: 78 - 79: 3.284 distance: 78 - 81: 26.267 distance: 79 - 80: 25.502 distance: 79 - 86: 13.930 distance: 81 - 82: 33.378 distance: 82 - 83: 10.115 distance: 83 - 84: 22.519 distance: 83 - 85: 25.691 distance: 86 - 87: 17.312 distance: 87 - 88: 17.180 distance: 88 - 89: 44.076 distance: 88 - 90: 18.232 distance: 90 - 91: 12.450 distance: 91 - 92: 14.579 distance: 91 - 94: 22.646 distance: 92 - 93: 11.639 distance: 92 - 98: 9.534 distance: 94 - 95: 14.383 distance: 95 - 96: 15.428 distance: 95 - 97: 39.784 distance: 98 - 99: 15.472 distance: 99 - 100: 9.190 distance: 99 - 102: 13.354 distance: 100 - 101: 39.895 distance: 100 - 104: 19.961 distance: 102 - 103: 41.582 distance: 104 - 105: 10.224 distance: 105 - 106: 40.118 distance: 105 - 108: 22.272 distance: 106 - 107: 43.359 distance: 106 - 110: 39.384 distance: 108 - 109: 37.441 distance: 110 - 111: 8.076 distance: 110 - 116: 21.115 distance: 111 - 112: 12.518 distance: 111 - 114: 17.012 distance: 112 - 113: 9.969 distance: 112 - 117: 22.101 distance: 114 - 115: 20.668 distance: 115 - 116: 28.721 distance: 117 - 118: 6.930 distance: 118 - 119: 15.843 distance: 118 - 121: 23.558 distance: 119 - 120: 16.026 distance: 119 - 124: 23.578 distance: 121 - 122: 19.175 distance: 121 - 123: 13.700 distance: 124 - 125: 16.544 distance: 125 - 126: 7.572 distance: 125 - 128: 15.936 distance: 126 - 127: 17.943 distance: 126 - 131: 21.889 distance: 128 - 129: 27.654 distance: 128 - 130: 18.544 distance: 131 - 132: 31.803 distance: 132 - 133: 15.423 distance: 132 - 135: 18.293 distance: 133 - 134: 15.195 distance: 133 - 140: 13.996 distance: 135 - 136: 21.168 distance: 136 - 137: 26.137 distance: 137 - 138: 17.413 distance: 138 - 139: 12.837