Starting phenix.real_space_refine on Tue Jun 17 16:23:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vn0_21246/06_2025/6vn0_21246.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vn0_21246/06_2025/6vn0_21246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vn0_21246/06_2025/6vn0_21246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vn0_21246/06_2025/6vn0_21246.map" model { file = "/net/cci-nas-00/data/ceres_data/6vn0_21246/06_2025/6vn0_21246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vn0_21246/06_2025/6vn0_21246.cif" } resolution = 4.25 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= 0.003 sd= 0.051 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 126 5.16 5 C 12525 2.51 5 N 3306 2.21 5 O 4005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19962 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3378 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "B" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "H" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3378 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "E" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "G" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "J" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3378 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "I" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "K" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 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: "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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" 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: "B" 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: "C" 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: "E" 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: "D" 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: "F" 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: 12.63, per 1000 atoms: 0.63 Number of scatterers: 19962 At special positions: 0 Unit cell: (141.11, 145.23, 119.48, 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 126 16.00 O 4005 8.00 N 3306 7.00 C 12525 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.09 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.18 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.05 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.08 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.10 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.09 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.18 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.05 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.08 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.10 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.02 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.09 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.05 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.18 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.05 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.08 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.10 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " 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 Q 4 " - " MAN Q 5 " " MAN b 4 " - " MAN b 5 " " MAN m 4 " - " MAN m 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Q 3 " - " MAN Q 4 " " BMA X 3 " - " MAN X 4 " " BMA b 3 " - " MAN b 4 " " BMA i 3 " - " MAN i 4 " " BMA m 3 " - " MAN m 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA X 3 " - " MAN X 5 " " BMA i 3 " - " MAN i 5 " BETA1-4 " 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " 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 X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " 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 i 2 " - " BMA i 3 " " 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 p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " NAG-ASN " NAG A 619 " - " ASN A 295 " " NAG A 622 " - " ASN A 355 " " NAG A 629 " - " ASN A 133 " " NAG A 632 " - " ASN A 301 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 611 " " NAG C 619 " - " ASN C 295 " " NAG C 622 " - " ASN C 355 " " NAG C 629 " - " ASN C 133 " " NAG C 632 " - " ASN C 301 " " NAG D 619 " - " ASN D 295 " " NAG D 622 " - " ASN D 355 " " NAG D 629 " - " ASN D 133 " " NAG D 632 " - " ASN D 301 " " NAG E 701 " - " ASN E 618 " " NAG E 702 " - " ASN E 637 " " NAG E 703 " - " ASN E 611 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 611 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 156 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 234 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 197 " " NAG W 1 " - " ASN A 448 " " NAG X 1 " - " ASN C 88 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 276 " " NAG d 1 " - " ASN C 332 " " NAG e 1 " - " ASN C 386 " " NAG f 1 " - " ASN C 392 " " NAG g 1 " - " ASN C 197 " " NAG h 1 " - " ASN C 448 " " NAG i 1 " - " ASN D 88 " " NAG j 1 " - " ASN D 156 " " NAG k 1 " - " ASN D 160 " " NAG l 1 " - " ASN D 234 " " NAG m 1 " - " ASN D 262 " " NAG n 1 " - " ASN D 276 " " NAG o 1 " - " ASN D 332 " " NAG p 1 " - " ASN D 386 " " NAG q 1 " - " ASN D 392 " " NAG r 1 " - " ASN D 197 " " NAG s 1 " - " ASN D 448 " Time building additional restraints: 6.28 Conformation dependent library (CDL) restraints added in 2.2 seconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4362 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 23.1% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.043A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 5.134A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 528 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 597 removed outlier: 3.525A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 646 Processing helix chain 'B' and resid 648 through 661 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.043A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 476 through 484 removed outlier: 5.133A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 528 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 537 through 542 Processing helix chain 'E' and resid 547 through 551 Processing helix chain 'E' and resid 572 through 597 removed outlier: 3.525A pdb=" N LEU E 576 " --> pdb=" O GLY E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 626 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 646 Processing helix chain 'E' and resid 648 through 661 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 99 through 117 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 334 through 354 removed outlier: 4.043A pdb=" N LYS D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 476 through 484 removed outlier: 5.133A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 528 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'F' and resid 547 through 551 Processing helix chain 'F' and resid 572 through 597 removed outlier: 3.525A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 646 Processing helix chain 'F' and resid 648 through 661 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.158A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.317A 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 53 through 55 removed outlier: 5.513A pdb=" N ILE A 215 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY A 250 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR A 217 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.875A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.586A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.814A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.486A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.630A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.158A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 55 removed outlier: 5.514A pdb=" N ILE C 215 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY C 250 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR C 217 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.875A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC3, first strand: chain 'C' and resid 181 through 182 Processing sheet with id=AC4, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.586A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.814A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.486A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.630A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 13 Processing sheet with id=AD4, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.158A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'D' and resid 53 through 55 removed outlier: 5.513A pdb=" N ILE D 215 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY D 250 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR D 217 " --> pdb=" O THR D 248 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 91 through 94 removed outlier: 3.875A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 130 through 133 Processing sheet with id=AD9, first strand: chain 'D' and resid 181 through 182 Processing sheet with id=AE1, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.585A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.337A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.814A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.337A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 304 through 312 removed outlier: 6.486A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.487A pdb=" N ALA I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.630A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 795 hydrogen bonds defined for protein. 1980 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: 7.12 Time building geometry restraints manager: 7.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 5262 1.33 - 1.47: 6322 1.47 - 1.60: 8620 1.60 - 1.74: 13 1.74 - 1.88: 159 Bond restraints: 20376 Sorted by residual: bond pdb=" CB HIS I 32 " pdb=" CG HIS I 32 " ideal model delta sigma weight residual 1.497 1.435 0.062 1.40e-02 5.10e+03 1.94e+01 bond pdb=" CB HIS G 32 " pdb=" CG HIS G 32 " ideal model delta sigma weight residual 1.497 1.435 0.062 1.40e-02 5.10e+03 1.93e+01 bond pdb=" CB HIS H 32 " pdb=" CG HIS H 32 " ideal model delta sigma weight residual 1.497 1.436 0.061 1.40e-02 5.10e+03 1.91e+01 bond pdb=" CA PHE A 53 " pdb=" C PHE A 53 " ideal model delta sigma weight residual 1.522 1.473 0.050 1.19e-02 7.06e+03 1.73e+01 bond pdb=" CA PHE D 53 " pdb=" C PHE D 53 " ideal model delta sigma weight residual 1.522 1.473 0.050 1.19e-02 7.06e+03 1.73e+01 ... (remaining 20371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 23849 2.42 - 4.84: 3222 4.84 - 7.26: 530 7.26 - 9.68: 53 9.68 - 12.10: 3 Bond angle restraints: 27657 Sorted by residual: angle pdb=" N LEU B 520 " pdb=" CA LEU B 520 " pdb=" C LEU B 520 " ideal model delta sigma weight residual 113.50 101.40 12.10 1.23e+00 6.61e-01 9.69e+01 angle pdb=" N LEU E 520 " pdb=" CA LEU E 520 " pdb=" C LEU E 520 " ideal model delta sigma weight residual 113.50 101.42 12.08 1.23e+00 6.61e-01 9.65e+01 angle pdb=" N LEU F 520 " pdb=" CA LEU F 520 " pdb=" C LEU F 520 " ideal model delta sigma weight residual 113.50 101.45 12.05 1.23e+00 6.61e-01 9.60e+01 angle pdb=" C CYS C 239 " pdb=" N PRO C 240 " pdb=" CA PRO C 240 " ideal model delta sigma weight residual 119.56 127.26 -7.70 1.02e+00 9.61e-01 5.69e+01 angle pdb=" C CYS D 239 " pdb=" N PRO D 240 " pdb=" CA PRO D 240 " ideal model delta sigma weight residual 119.56 127.24 -7.68 1.02e+00 9.61e-01 5.66e+01 ... (remaining 27652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.51: 12984 22.51 - 45.01: 366 45.01 - 67.52: 87 67.52 - 90.02: 63 90.02 - 112.53: 24 Dihedral angle restraints: 13524 sinusoidal: 6747 harmonic: 6777 Sorted by residual: dihedral pdb=" CA CYS D 126 " pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " ideal model delta sinusoidal sigma weight residual 79.00 5.72 73.28 1 2.00e+01 2.50e-03 1.71e+01 dihedral pdb=" CA CYS A 126 " pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " ideal model delta sinusoidal sigma weight residual 79.00 5.73 73.27 1 2.00e+01 2.50e-03 1.71e+01 dihedral pdb=" CA CYS C 126 " pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " ideal model delta sinusoidal sigma weight residual 79.00 5.75 73.25 1 2.00e+01 2.50e-03 1.71e+01 ... (remaining 13521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2473 0.106 - 0.212: 821 0.212 - 0.319: 86 0.319 - 0.425: 1 0.425 - 0.531: 6 Chirality restraints: 3387 Sorted by residual: chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.43e+01 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.39e+01 chirality pdb=" C1 NAG p 2 " pdb=" O4 NAG p 1 " pdb=" C2 NAG p 2 " pdb=" O5 NAG p 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.29e+01 ... (remaining 3384 not shown) Planarity restraints: 3429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 611 " 0.076 2.00e-02 2.50e+03 7.95e-02 7.90e+01 pdb=" CG ASN E 611 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN E 611 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN E 611 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG E 703 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " 0.076 2.00e-02 2.50e+03 7.94e-02 7.89e+01 pdb=" CG ASN B 611 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG B 703 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 611 " 0.076 2.00e-02 2.50e+03 7.94e-02 7.88e+01 pdb=" CG ASN F 611 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN F 611 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN F 611 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG F 703 " 0.095 2.00e-02 2.50e+03 ... (remaining 3426 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5065 2.80 - 3.32: 17794 3.32 - 3.85: 33633 3.85 - 4.37: 39409 4.37 - 4.90: 63111 Nonbonded interactions: 159012 Sorted by model distance: nonbonded pdb=" O3 NAG M 1 " pdb=" O7 NAG M 1 " model vdw 2.270 3.040 nonbonded pdb=" O3 NAG i 1 " pdb=" O7 NAG i 1 " model vdw 2.270 3.040 nonbonded pdb=" O3 NAG X 1 " pdb=" O7 NAG X 1 " model vdw 2.270 3.040 nonbonded pdb=" N ASN A 355 " pdb=" OD1 ASN A 355 " model vdw 2.308 3.120 nonbonded pdb=" N ASN C 355 " pdb=" OD1 ASN C 355 " model vdw 2.308 3.120 ... (remaining 159007 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'X' selection = chain 'b' selection = chain 'i' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 48.060 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.170 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 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 : 0.019 0.145 20520 Z= 0.985 Angle : 1.779 12.105 28050 Z= 1.123 Chirality : 0.098 0.531 3387 Planarity : 0.009 0.049 3375 Dihedral : 12.940 112.525 9045 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.65 % Allowed : 2.86 % Favored : 96.49 % Rotamer: Outliers : 0.15 % Allowed : 1.02 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.70 (0.17), residues: 2310 helix: -0.39 (0.24), residues: 390 sheet: 1.07 (0.20), residues: 630 loop : 0.58 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.010 TRP E 571 HIS 0.017 0.004 HIS D 374 PHE 0.040 0.007 PHE E 522 TYR 0.060 0.009 TYR E 638 ARG 0.005 0.001 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.02955 ( 54) link_NAG-ASN : angle 2.16018 ( 162) link_ALPHA1-6 : bond 0.03315 ( 3) link_ALPHA1-6 : angle 2.36337 ( 9) link_BETA1-4 : bond 0.03475 ( 39) link_BETA1-4 : angle 3.33177 ( 117) link_ALPHA1-2 : bond 0.04085 ( 3) link_ALPHA1-2 : angle 2.35557 ( 9) link_ALPHA1-3 : bond 0.04231 ( 6) link_ALPHA1-3 : angle 3.46683 ( 18) hydrogen bonds : bond 0.19258 ( 747) hydrogen bonds : angle 8.16803 ( 1980) SS BOND : bond 0.05049 ( 39) SS BOND : angle 2.96607 ( 78) covalent geometry : bond 0.01834 (20376) covalent geometry : angle 1.76049 (27657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 815 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8629 (mt) cc_final: 0.8167 (mm) REVERT: A 116 LEU cc_start: 0.8467 (mt) cc_final: 0.7952 (mt) REVERT: A 373 THR cc_start: 0.8850 (p) cc_final: 0.8389 (p) REVERT: A 450 THR cc_start: 0.8386 (p) cc_final: 0.7688 (t) REVERT: B 586 TYR cc_start: 0.9136 (t80) cc_final: 0.8526 (t80) REVERT: B 604 CYS cc_start: 0.5202 (t) cc_final: 0.4887 (t) REVERT: H 25 SER cc_start: 0.7152 (t) cc_final: 0.5102 (p) REVERT: L 10 PHE cc_start: 0.7351 (p90) cc_final: 0.7096 (p90) REVERT: L 92 ASN cc_start: 0.8912 (t0) cc_final: 0.8371 (t0) REVERT: C 52 LEU cc_start: 0.8588 (mt) cc_final: 0.8210 (mm) REVERT: C 116 LEU cc_start: 0.8643 (mt) cc_final: 0.8272 (mt) REVERT: C 217 TYR cc_start: 0.8203 (m-80) cc_final: 0.7581 (m-80) REVERT: C 251 ILE cc_start: 0.9410 (mt) cc_final: 0.9185 (tp) REVERT: C 373 THR cc_start: 0.8858 (p) cc_final: 0.8399 (p) REVERT: C 450 THR cc_start: 0.8362 (p) cc_final: 0.7672 (t) REVERT: E 584 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8508 (mt-10) REVERT: E 610 TRP cc_start: 0.8569 (t-100) cc_final: 0.8140 (t-100) REVERT: E 643 TYR cc_start: 0.8749 (m-10) cc_final: 0.8544 (m-80) REVERT: G 25 SER cc_start: 0.7059 (t) cc_final: 0.5131 (p) REVERT: J 10 PHE cc_start: 0.7430 (p90) cc_final: 0.7157 (p90) REVERT: D 42 VAL cc_start: 0.9486 (t) cc_final: 0.9286 (p) REVERT: D 52 LEU cc_start: 0.8583 (mt) cc_final: 0.8139 (mm) REVERT: D 107 ASP cc_start: 0.8614 (m-30) cc_final: 0.8379 (p0) REVERT: D 114 GLN cc_start: 0.8831 (tp40) cc_final: 0.8609 (tm-30) REVERT: D 217 TYR cc_start: 0.8344 (m-80) cc_final: 0.7421 (m-80) REVERT: D 373 THR cc_start: 0.8822 (p) cc_final: 0.8575 (p) REVERT: D 450 THR cc_start: 0.8213 (p) cc_final: 0.7535 (t) REVERT: F 543 ASN cc_start: 0.8871 (m-40) cc_final: 0.8595 (t0) REVERT: F 584 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8258 (mt-10) REVERT: I 25 SER cc_start: 0.6930 (t) cc_final: 0.4800 (p) REVERT: K 10 PHE cc_start: 0.7492 (p90) cc_final: 0.7255 (p90) REVERT: K 92 ASN cc_start: 0.8832 (t0) cc_final: 0.8583 (t0) outliers start: 3 outliers final: 3 residues processed: 818 average time/residue: 0.3889 time to fit residues: 482.2434 Evaluate side-chains 432 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 429 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 92 optimal weight: 0.0170 chunk 178 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 overall best weight: 0.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 550 GLN H 32 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 76 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 550 GLN ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 HIS G 35 HIS G 39 GLN J 76 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 HIS I 39 GLN K 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.075991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.062147 restraints weight = 71592.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.064692 restraints weight = 38852.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.066509 restraints weight = 25200.103| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20520 Z= 0.181 Angle : 0.867 11.263 28050 Z= 0.424 Chirality : 0.050 0.365 3387 Planarity : 0.005 0.035 3375 Dihedral : 8.668 63.808 4689 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.64 % Favored : 95.84 % Rotamer: Outliers : 0.05 % Allowed : 2.52 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.46 (0.17), residues: 2310 helix: 0.53 (0.27), residues: 390 sheet: 0.98 (0.19), residues: 675 loop : -0.07 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 610 HIS 0.010 0.002 HIS D 105 PHE 0.036 0.003 PHE K 71 TYR 0.027 0.002 TYR I 100I ARG 0.007 0.001 ARG D 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 54) link_NAG-ASN : angle 3.36258 ( 162) link_ALPHA1-6 : bond 0.00742 ( 3) link_ALPHA1-6 : angle 1.55960 ( 9) link_BETA1-4 : bond 0.00549 ( 39) link_BETA1-4 : angle 2.56657 ( 117) link_ALPHA1-2 : bond 0.00756 ( 3) link_ALPHA1-2 : angle 1.59398 ( 9) link_ALPHA1-3 : bond 0.00885 ( 6) link_ALPHA1-3 : angle 2.12187 ( 18) hydrogen bonds : bond 0.06032 ( 747) hydrogen bonds : angle 6.30868 ( 1980) SS BOND : bond 0.00665 ( 39) SS BOND : angle 1.14192 ( 78) covalent geometry : bond 0.00399 (20376) covalent geometry : angle 0.81270 (27657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 601 time to evaluate : 4.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8539 (mmp) cc_final: 0.8339 (tpp) REVERT: A 215 ILE cc_start: 0.8951 (tp) cc_final: 0.8751 (tt) REVERT: A 217 TYR cc_start: 0.7297 (m-80) cc_final: 0.7032 (m-80) REVERT: A 256 SER cc_start: 0.8227 (p) cc_final: 0.7943 (p) REVERT: A 373 THR cc_start: 0.8782 (p) cc_final: 0.8481 (t) REVERT: B 543 ASN cc_start: 0.9283 (t0) cc_final: 0.8913 (t0) REVERT: B 586 TYR cc_start: 0.8841 (t80) cc_final: 0.8420 (t80) REVERT: B 606 THR cc_start: 0.8681 (p) cc_final: 0.8421 (p) REVERT: B 626 MET cc_start: 0.9106 (mmp) cc_final: 0.8715 (mmm) REVERT: B 653 GLN cc_start: 0.9213 (tt0) cc_final: 0.8931 (mp10) REVERT: H 18 LEU cc_start: 0.7843 (tt) cc_final: 0.7135 (tt) REVERT: H 58 TYR cc_start: 0.9208 (m-10) cc_final: 0.8911 (m-10) REVERT: H 61 ASP cc_start: 0.9188 (p0) cc_final: 0.8952 (p0) REVERT: L 37 GLN cc_start: 0.8918 (pp30) cc_final: 0.8508 (pp30) REVERT: L 53 GLN cc_start: 0.8690 (tp40) cc_final: 0.8433 (tp-100) REVERT: L 82 ASP cc_start: 0.8032 (m-30) cc_final: 0.7819 (m-30) REVERT: C 36 VAL cc_start: 0.9313 (t) cc_final: 0.9107 (t) REVERT: C 157 CYS cc_start: 0.7227 (m) cc_final: 0.7002 (m) REVERT: C 256 SER cc_start: 0.7373 (t) cc_final: 0.7048 (t) REVERT: C 373 THR cc_start: 0.8831 (p) cc_final: 0.8514 (t) REVERT: C 387 THR cc_start: 0.9561 (p) cc_final: 0.9270 (t) REVERT: C 435 TYR cc_start: 0.8033 (t80) cc_final: 0.7785 (t80) REVERT: E 529 THR cc_start: 0.8933 (p) cc_final: 0.8687 (t) REVERT: E 543 ASN cc_start: 0.9250 (t0) cc_final: 0.8853 (t0) REVERT: E 545 LEU cc_start: 0.8765 (tp) cc_final: 0.8352 (tt) REVERT: E 586 TYR cc_start: 0.8912 (t80) cc_final: 0.8364 (t80) REVERT: E 588 ARG cc_start: 0.9171 (ttp80) cc_final: 0.8942 (ttp80) REVERT: E 591 GLN cc_start: 0.9436 (tp40) cc_final: 0.8788 (tp40) REVERT: E 606 THR cc_start: 0.8658 (p) cc_final: 0.8416 (p) REVERT: E 626 MET cc_start: 0.9115 (mmp) cc_final: 0.8771 (mmm) REVERT: G 20 LEU cc_start: 0.9164 (mt) cc_final: 0.8831 (mp) REVERT: G 61 ASP cc_start: 0.9050 (p0) cc_final: 0.8703 (p0) REVERT: J 10 PHE cc_start: 0.7406 (p90) cc_final: 0.7195 (p90) REVERT: J 37 GLN cc_start: 0.8988 (pp30) cc_final: 0.8781 (pp30) REVERT: J 53 GLN cc_start: 0.8730 (tp40) cc_final: 0.8503 (tp-100) REVERT: J 82 ASP cc_start: 0.7928 (m-30) cc_final: 0.7642 (m-30) REVERT: D 42 VAL cc_start: 0.9423 (t) cc_final: 0.9106 (p) REVERT: D 107 ASP cc_start: 0.9186 (m-30) cc_final: 0.8789 (p0) REVERT: D 114 GLN cc_start: 0.9370 (tp40) cc_final: 0.8881 (tm-30) REVERT: D 217 TYR cc_start: 0.7972 (m-80) cc_final: 0.7332 (m-80) REVERT: D 256 SER cc_start: 0.7548 (t) cc_final: 0.7235 (t) REVERT: D 373 THR cc_start: 0.8802 (p) cc_final: 0.8461 (t) REVERT: D 435 TYR cc_start: 0.8250 (t80) cc_final: 0.7954 (t80) REVERT: F 529 THR cc_start: 0.8902 (p) cc_final: 0.8423 (t) REVERT: F 591 GLN cc_start: 0.9395 (tp40) cc_final: 0.9165 (tp40) REVERT: F 606 THR cc_start: 0.8725 (p) cc_final: 0.8475 (p) REVERT: F 626 MET cc_start: 0.9134 (mmp) cc_final: 0.8560 (mmm) REVERT: I 18 LEU cc_start: 0.7958 (tt) cc_final: 0.7084 (tt) REVERT: I 34 MET cc_start: 0.8744 (mmm) cc_final: 0.8484 (mmm) REVERT: I 58 TYR cc_start: 0.9225 (m-10) cc_final: 0.8743 (m-10) REVERT: I 61 ASP cc_start: 0.8983 (p0) cc_final: 0.8697 (p0) REVERT: K 33 LEU cc_start: 0.8592 (tp) cc_final: 0.8044 (tp) REVERT: K 53 GLN cc_start: 0.8840 (tp40) cc_final: 0.8607 (tp-100) REVERT: K 78 LEU cc_start: 0.9231 (tp) cc_final: 0.8948 (tp) outliers start: 1 outliers final: 0 residues processed: 601 average time/residue: 0.3456 time to fit residues: 341.7469 Evaluate side-chains 441 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 27 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 147 optimal weight: 0.0000 chunk 18 optimal weight: 0.6980 chunk 181 optimal weight: 0.8980 chunk 148 optimal weight: 20.0000 chunk 137 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS J 6 GLN J 24 GLN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN K 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.073518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.060077 restraints weight = 71109.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.062482 restraints weight = 38338.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.064187 restraints weight = 24842.489| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20520 Z= 0.153 Angle : 0.763 13.531 28050 Z= 0.370 Chirality : 0.046 0.296 3387 Planarity : 0.004 0.070 3375 Dihedral : 6.955 47.596 4689 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.42 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.36 (0.17), residues: 2310 helix: 0.46 (0.26), residues: 408 sheet: 0.79 (0.18), residues: 684 loop : -0.07 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 112 HIS 0.008 0.001 HIS D 105 PHE 0.021 0.002 PHE H 100J TYR 0.014 0.001 TYR H 100I ARG 0.013 0.001 ARG F 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 54) link_NAG-ASN : angle 3.09580 ( 162) link_ALPHA1-6 : bond 0.00838 ( 3) link_ALPHA1-6 : angle 1.89282 ( 9) link_BETA1-4 : bond 0.00498 ( 39) link_BETA1-4 : angle 2.01364 ( 117) link_ALPHA1-2 : bond 0.00652 ( 3) link_ALPHA1-2 : angle 1.68215 ( 9) link_ALPHA1-3 : bond 0.01146 ( 6) link_ALPHA1-3 : angle 1.11233 ( 18) hydrogen bonds : bond 0.04866 ( 747) hydrogen bonds : angle 5.93355 ( 1980) SS BOND : bond 0.00647 ( 39) SS BOND : angle 0.98291 ( 78) covalent geometry : bond 0.00336 (20376) covalent geometry : angle 0.71574 (27657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 533 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.8605 (m-40) cc_final: 0.8292 (p0) REVERT: A 136 ASN cc_start: 0.8498 (m-40) cc_final: 0.8106 (m110) REVERT: A 211 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7335 (tm-30) REVERT: A 217 TYR cc_start: 0.7634 (m-80) cc_final: 0.7359 (m-10) REVERT: B 529 THR cc_start: 0.8883 (p) cc_final: 0.8551 (t) REVERT: B 543 ASN cc_start: 0.9323 (t0) cc_final: 0.8932 (t0) REVERT: B 586 TYR cc_start: 0.8730 (t80) cc_final: 0.8407 (t80) REVERT: B 593 LEU cc_start: 0.9667 (tp) cc_final: 0.9401 (tp) REVERT: B 653 GLN cc_start: 0.9366 (tt0) cc_final: 0.9059 (mp10) REVERT: H 18 LEU cc_start: 0.8008 (tt) cc_final: 0.7383 (tt) REVERT: H 27 PHE cc_start: 0.7337 (p90) cc_final: 0.6938 (p90) REVERT: H 49 SER cc_start: 0.9070 (p) cc_final: 0.8853 (t) REVERT: H 58 TYR cc_start: 0.9334 (m-10) cc_final: 0.9114 (m-10) REVERT: H 69 ILE cc_start: 0.9458 (tp) cc_final: 0.9175 (tp) REVERT: H 100 TYR cc_start: 0.8384 (t80) cc_final: 0.7924 (t80) REVERT: L 37 GLN cc_start: 0.8879 (pp30) cc_final: 0.8613 (pp30) REVERT: C 67 ASN cc_start: 0.8595 (p0) cc_final: 0.8377 (p0) REVERT: C 116 LEU cc_start: 0.8563 (mt) cc_final: 0.8362 (mt) REVERT: C 136 ASN cc_start: 0.8470 (m-40) cc_final: 0.8104 (m110) REVERT: C 211 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7683 (tm-30) REVERT: C 434 MET cc_start: 0.8225 (mpp) cc_final: 0.7847 (mpp) REVERT: C 435 TYR cc_start: 0.8191 (t80) cc_final: 0.7608 (t80) REVERT: C 454 LEU cc_start: 0.9694 (mp) cc_final: 0.9428 (mt) REVERT: E 543 ASN cc_start: 0.9286 (t0) cc_final: 0.8994 (t0) REVERT: E 545 LEU cc_start: 0.8872 (tp) cc_final: 0.8492 (tt) REVERT: E 586 TYR cc_start: 0.8871 (t80) cc_final: 0.8333 (t80) REVERT: E 591 GLN cc_start: 0.9500 (tp40) cc_final: 0.9004 (tp40) REVERT: E 626 MET cc_start: 0.9225 (mmp) cc_final: 0.8778 (mmm) REVERT: E 632 ASP cc_start: 0.9292 (t70) cc_final: 0.9019 (t70) REVERT: G 18 LEU cc_start: 0.7767 (tt) cc_final: 0.7147 (tt) REVERT: G 20 LEU cc_start: 0.9271 (mt) cc_final: 0.8917 (mp) REVERT: G 49 SER cc_start: 0.9156 (p) cc_final: 0.8756 (t) REVERT: G 61 ASP cc_start: 0.9080 (p0) cc_final: 0.8773 (p0) REVERT: G 69 ILE cc_start: 0.9370 (tp) cc_final: 0.9044 (tp) REVERT: J 32 ASN cc_start: 0.9068 (m-40) cc_final: 0.8860 (m-40) REVERT: J 53 GLN cc_start: 0.8791 (tp40) cc_final: 0.8535 (tp-100) REVERT: D 42 VAL cc_start: 0.9465 (t) cc_final: 0.9118 (p) REVERT: D 104 MET cc_start: 0.9600 (ttm) cc_final: 0.9352 (ttm) REVERT: D 107 ASP cc_start: 0.9203 (m-30) cc_final: 0.8836 (m-30) REVERT: D 114 GLN cc_start: 0.9364 (tp40) cc_final: 0.8961 (tm-30) REVERT: D 116 LEU cc_start: 0.8732 (mt) cc_final: 0.8493 (mt) REVERT: D 136 ASN cc_start: 0.8490 (m-40) cc_final: 0.8062 (m110) REVERT: D 195 ASN cc_start: 0.8709 (p0) cc_final: 0.8504 (p0) REVERT: D 211 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7048 (tm-30) REVERT: D 256 SER cc_start: 0.7478 (t) cc_final: 0.7103 (t) REVERT: D 435 TYR cc_start: 0.8232 (t80) cc_final: 0.7713 (t80) REVERT: F 539 VAL cc_start: 0.9828 (t) cc_final: 0.9604 (p) REVERT: F 543 ASN cc_start: 0.9359 (t0) cc_final: 0.9001 (t0) REVERT: F 549 VAL cc_start: 0.8119 (m) cc_final: 0.7555 (t) REVERT: F 591 GLN cc_start: 0.9438 (tp40) cc_final: 0.9131 (tp40) REVERT: F 621 GLU cc_start: 0.8477 (tp30) cc_final: 0.7818 (tp30) REVERT: I 18 LEU cc_start: 0.7786 (tt) cc_final: 0.7275 (tt) REVERT: I 47 TRP cc_start: 0.8458 (t60) cc_final: 0.8217 (t60) REVERT: I 100 TYR cc_start: 0.7944 (t80) cc_final: 0.7652 (t80) REVERT: K 37 GLN cc_start: 0.8996 (pp30) cc_final: 0.8746 (pp30) REVERT: K 78 LEU cc_start: 0.9307 (tp) cc_final: 0.9084 (tp) REVERT: K 87 TYR cc_start: 0.8781 (m-80) cc_final: 0.8531 (m-80) outliers start: 0 outliers final: 0 residues processed: 533 average time/residue: 0.3274 time to fit residues: 283.3912 Evaluate side-chains 405 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 4.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 73.1127 > 50: distance: 11 - 33: 21.685 distance: 17 - 41: 34.957 distance: 21 - 49: 32.215 distance: 27 - 33: 24.916 distance: 28 - 53: 37.184 distance: 33 - 34: 33.195 distance: 34 - 37: 40.264 distance: 35 - 36: 57.128 distance: 36 - 61: 38.216 distance: 37 - 38: 44.618 distance: 38 - 39: 41.088 distance: 38 - 40: 23.307 distance: 41 - 42: 16.206 distance: 42 - 43: 46.817 distance: 42 - 45: 29.741 distance: 44 - 75: 58.242 distance: 45 - 46: 46.552 distance: 46 - 47: 40.254 distance: 49 - 50: 46.573 distance: 50 - 51: 17.364 distance: 51 - 52: 21.910 distance: 51 - 53: 34.244 distance: 53 - 54: 51.407 distance: 54 - 55: 6.744 distance: 54 - 57: 8.672 distance: 55 - 56: 38.855 distance: 55 - 61: 34.455 distance: 57 - 58: 40.375 distance: 57 - 59: 38.529 distance: 58 - 60: 40.396 distance: 61 - 62: 7.512 distance: 62 - 63: 56.068 distance: 62 - 65: 56.097 distance: 63 - 64: 57.164 distance: 63 - 75: 39.339 distance: 66 - 67: 38.677 distance: 66 - 68: 9.318 distance: 67 - 69: 33.655 distance: 68 - 70: 13.517 distance: 68 - 71: 23.197 distance: 69 - 70: 11.058 distance: 70 - 72: 31.630 distance: 71 - 73: 40.091 distance: 72 - 74: 16.246 distance: 73 - 74: 37.672 distance: 75 - 76: 48.443 distance: 76 - 77: 15.097 distance: 77 - 79: 38.885 distance: 80 - 83: 57.479 distance: 81 - 82: 56.987 distance: 81 - 85: 39.671 distance: 83 - 84: 56.554 distance: 84 - 119: 34.295 distance: 86 - 87: 56.598 distance: 86 - 89: 39.819 distance: 87 - 88: 56.831 distance: 87 - 91: 41.092 distance: 89 - 90: 39.306 distance: 92 - 93: 12.080 distance: 93 - 94: 39.847 distance: 93 - 95: 56.744 distance: 96 - 99: 33.576 distance: 97 - 104: 34.208 distance: 99 - 100: 43.456 distance: 100 - 101: 42.939 distance: 101 - 102: 23.779