Starting phenix.real_space_refine on Sat May 24 22:35:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bew_44484/05_2025/9bew_44484.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bew_44484/05_2025/9bew_44484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bew_44484/05_2025/9bew_44484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bew_44484/05_2025/9bew_44484.map" model { file = "/net/cci-nas-00/data/ceres_data/9bew_44484/05_2025/9bew_44484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bew_44484/05_2025/9bew_44484.cif" } resolution = 3.3 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= 0.015 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 141 5.16 5 C 16326 2.51 5 N 4389 2.21 5 O 5244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 210 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26100 Number of models: 1 Model: "" Number of chains: 51 Chain: "G" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3481 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1008 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 767 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "H" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "A" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3481 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1008 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "F" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "I" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 767 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "J" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "K" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "M" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3481 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1008 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "O" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "P" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 767 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "Q" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "R" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} 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: 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: "W" 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: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "a" Number of atoms: 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: 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: "f" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} 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: "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: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} 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: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: "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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: "I" 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: "M" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: "P" 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 Time building chain proxies: 16.37, per 1000 atoms: 0.63 Number of scatterers: 26100 At special positions: 0 Unit cell: (158.934, 150.166, 153.454, 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 141 16.00 O 5244 8.00 N 4389 7.00 C 16326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 429A" 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 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 B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 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 A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 429A" 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 218 " - pdb=" SG CYS A 247 " distance=2.04 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 E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 54 " - pdb=" SG CYS M 74 " distance=2.03 Simple disulfide: pdb=" SG CYS M 113 " - pdb=" SG CYS M 429A" distance=2.03 Simple disulfide: pdb=" SG CYS M 119 " - pdb=" SG CYS M 205 " distance=2.04 Simple disulfide: pdb=" SG CYS M 126 " - pdb=" SG CYS M 196 " distance=2.03 Simple disulfide: pdb=" SG CYS M 131 " - pdb=" SG CYS M 157 " distance=2.03 Simple disulfide: pdb=" SG CYS M 218 " - pdb=" SG CYS M 247 " distance=2.04 Simple disulfide: pdb=" SG CYS M 228 " - pdb=" SG CYS M 239 " distance=2.03 Simple disulfide: pdb=" SG CYS M 296 " - pdb=" SG CYS M 331 " distance=2.03 Simple disulfide: pdb=" SG CYS M 378 " - pdb=" SG CYS M 445 " distance=2.03 Simple disulfide: pdb=" SG CYS M 385 " - pdb=" SG CYS M 418 " distance=2.03 Simple disulfide: pdb=" SG CYS N 598 " - pdb=" SG CYS N 604 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 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 V 4 " - " MAN V 5 " " MAN Z 4 " - " MAN Z 5 " " MAN Z 5 " - " MAN Z 6 " " MAN d 4 " - " MAN d 5 " " MAN h 4 " - " MAN h 5 " " MAN h 5 " - " MAN h 6 " " MAN l 4 " - " MAN l 5 " " MAN p 4 " - " MAN p 5 " " MAN p 5 " - " MAN p 6 " ALPHA1-3 " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 7 " - " MAN Z 8 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " " BMA h 3 " - " MAN h 4 " " MAN h 7 " - " MAN h 8 " " BMA l 3 " - " MAN l 4 " " BMA m 3 " - " MAN m 4 " " BMA p 3 " - " MAN p 4 " " MAN p 7 " - " MAN p 8 " ALPHA1-6 " BMA V 3 " - " MAN V 6 " " BMA W 3 " - " MAN W 5 " " BMA X 3 " - " MAN X 4 " " BMA Z 3 " - " MAN Z 7 " " MAN Z 7 " - " MAN Z 9 " " BMA d 3 " - " MAN d 6 " " BMA e 3 " - " MAN e 5 " " BMA f 3 " - " MAN f 4 " " BMA h 3 " - " MAN h 7 " " MAN h 7 " - " MAN h 9 " " BMA l 3 " - " MAN l 6 " " BMA m 3 " - " MAN m 5 " " BMA n 3 " - " MAN n 4 " " BMA p 3 " - " MAN p 7 " " MAN p 7 " - " MAN p 9 " BETA1-4 " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " 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 Z 2 " - " BMA Z 3 " " 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 f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " 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 l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 295 " " NAG A 606 " - " ASN A 301 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 355 " " NAG A 609 " - " ASN A 392 " " NAG A 610 " - " ASN A 241 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG D 301 " - " ASN D 72 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 234 " " NAG G 604 " - " ASN G 276 " " NAG G 605 " - " ASN G 295 " " NAG G 606 " - " ASN G 301 " " NAG G 607 " - " ASN G 339 " " NAG G 608 " - " ASN G 355 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 241 " " NAG I 301 " - " ASN I 72 " " NAG M 601 " - " ASN M 88 " " NAG M 602 " - " ASN M 133 " " NAG M 603 " - " ASN M 234 " " NAG M 604 " - " ASN M 276 " " NAG M 605 " - " ASN M 295 " " NAG M 606 " - " ASN M 301 " " NAG M 607 " - " ASN M 339 " " NAG M 608 " - " ASN M 355 " " NAG M 609 " - " ASN M 392 " " NAG M 610 " - " ASN M 241 " " NAG N 701 " - " ASN N 611 " " NAG N 702 " - " ASN N 637 " " NAG P 301 " - " ASN P 72 " " NAG S 1 " - " ASN G 156 " " NAG T 1 " - " ASN G 160 " " NAG U 1 " - " ASN G 197 " " NAG V 1 " - " ASN G 262 " " NAG W 1 " - " ASN G 363 " " NAG X 1 " - " ASN G 386 " " NAG Y 1 " - " ASN G 448 " " NAG Z 1 " - " ASN G 332 " " NAG a 1 " - " ASN A 156 " " NAG b 1 " - " ASN A 160 " " NAG c 1 " - " ASN A 197 " " NAG d 1 " - " ASN A 262 " " NAG e 1 " - " ASN A 363 " " NAG f 1 " - " ASN A 386 " " NAG g 1 " - " ASN A 448 " " NAG h 1 " - " ASN A 332 " " NAG i 1 " - " ASN M 156 " " NAG j 1 " - " ASN M 160 " " NAG k 1 " - " ASN M 197 " " NAG l 1 " - " ASN M 262 " " NAG m 1 " - " ASN M 363 " " NAG n 1 " - " ASN M 386 " " NAG o 1 " - " ASN M 448 " " NAG p 1 " - " ASN M 332 " Time building additional restraints: 7.90 Conformation dependent library (CDL) restraints added in 3.2 seconds 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5694 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 54 sheets defined 15.1% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'G' and resid 98 through 113 removed outlier: 4.049A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 4.178A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 350 removed outlier: 3.569A pdb=" N LYS G 344 " --> pdb=" O GLU G 340 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG G 350 " --> pdb=" O VAL G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.572A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 381 removed outlier: 3.549A pdb=" N GLY G 380 " --> pdb=" O ASN G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 429B removed outlier: 3.535A pdb=" N CYS G 429A" --> pdb=" O MET G 426 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY G 429B" --> pdb=" O TRP G 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 426 through 429B' Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.739A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 removed outlier: 3.517A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 566 through 570 Processing helix chain 'B' and resid 573 through 597 removed outlier: 3.823A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.519A pdb=" N ASP B 632 " --> pdb=" O TRP B 628 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 658 removed outlier: 3.577A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.755A pdb=" N ASP C 31 " --> pdb=" O ASN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.819A pdb=" N GLN C 64 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.804A pdb=" N ASP C 86 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 4.231A 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 'H' and resid 61 through 64 Processing helix chain 'A' and resid 98 through 113 removed outlier: 4.049A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.179A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.570A pdb=" N LYS A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.572A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.550A pdb=" N GLY A 380 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 429B removed outlier: 3.535A pdb=" N CYS A 429A" --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY A 429B" --> pdb=" O TRP A 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 426 through 429B' Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.739A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 537 through 542 removed outlier: 3.518A pdb=" N ARG E 542 " --> pdb=" O THR E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 545 No H-bonds generated for 'chain 'E' and resid 543 through 545' Processing helix chain 'E' and resid 566 through 570 Processing helix chain 'E' and resid 573 through 597 removed outlier: 3.823A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.519A pdb=" N ASP E 632 " --> pdb=" O TRP E 628 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 658 removed outlier: 3.577A pdb=" N ILE E 642 " --> pdb=" O TYR E 638 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR E 643 " --> pdb=" O THR E 639 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU E 647 " --> pdb=" O TYR E 643 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN E 650 " --> pdb=" O LEU E 646 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN E 651 " --> pdb=" O GLU E 647 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN E 652 " --> pdb=" O GLU E 648 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN E 656 " --> pdb=" O GLN E 652 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU E 657 " --> pdb=" O GLN E 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.755A pdb=" N ASP F 31 " --> pdb=" O ASN F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 64 removed outlier: 3.819A pdb=" N GLN F 64 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.805A pdb=" N ASP F 86 " --> pdb=" O ARG F 83 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 83 through 87' Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'M' and resid 98 through 113 removed outlier: 4.050A pdb=" N GLU M 102 " --> pdb=" O ASN M 98 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR M 106 " --> pdb=" O GLU M 102 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE M 109 " --> pdb=" O HIS M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 126 removed outlier: 4.178A pdb=" N CYS M 126 " --> pdb=" O THR M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 350 removed outlier: 3.569A pdb=" N LYS M 344 " --> pdb=" O GLU M 340 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS M 347 " --> pdb=" O GLY M 343 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG M 350 " --> pdb=" O VAL M 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 373 removed outlier: 3.573A pdb=" N THR M 373 " --> pdb=" O LEU M 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 381 removed outlier: 3.549A pdb=" N GLY M 380 " --> pdb=" O ASN M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 426 through 429B removed outlier: 3.535A pdb=" N CYS M 429A" --> pdb=" O MET M 426 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY M 429B" --> pdb=" O TRP M 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 426 through 429B' Processing helix chain 'M' and resid 476 through 481 removed outlier: 3.739A pdb=" N SER M 481 " --> pdb=" O ASP M 477 " (cutoff:3.500A) Processing helix chain 'N' and resid 529 through 534 Processing helix chain 'N' and resid 537 through 542 removed outlier: 3.517A pdb=" N ARG N 542 " --> pdb=" O THR N 538 " (cutoff:3.500A) Processing helix chain 'N' and resid 543 through 545 No H-bonds generated for 'chain 'N' and resid 543 through 545' Processing helix chain 'N' and resid 566 through 570 Processing helix chain 'N' and resid 573 through 597 removed outlier: 3.824A pdb=" N ASP N 589 " --> pdb=" O ARG N 585 " (cutoff:3.500A) Processing helix chain 'N' and resid 627 through 636 removed outlier: 3.519A pdb=" N ASP N 632 " --> pdb=" O TRP N 628 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS N 633 " --> pdb=" O LEU N 629 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU N 634 " --> pdb=" O GLN N 630 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE N 635 " --> pdb=" O TRP N 631 " (cutoff:3.500A) Processing helix chain 'N' and resid 638 through 658 removed outlier: 3.577A pdb=" N ILE N 642 " --> pdb=" O TYR N 638 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR N 643 " --> pdb=" O THR N 639 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU N 647 " --> pdb=" O TYR N 643 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN N 650 " --> pdb=" O LEU N 646 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN N 651 " --> pdb=" O GLU N 647 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN N 652 " --> pdb=" O GLU N 648 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN N 656 " --> pdb=" O GLN N 652 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU N 657 " --> pdb=" O GLN N 653 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.757A pdb=" N ASP O 31 " --> pdb=" O ASN O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 64 removed outlier: 3.819A pdb=" N GLN O 64 " --> pdb=" O ARG O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.805A pdb=" N ASP O 86 " --> pdb=" O ARG O 83 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR O 87 " --> pdb=" O SER O 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 83 through 87' Processing helix chain 'Q' and resid 61 through 64 Processing sheet with id=AA1, first strand: chain 'G' and resid 494 through 499 removed outlier: 5.772A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.960A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU G 86 " --> pdb=" O VAL G 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 75 through 76 removed outlier: 7.157A pdb=" N CYS G 54 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.538A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'G' and resid 181 through 183 removed outlier: 3.564A pdb=" N VAL G 182 " --> pdb=" O ARG G 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 201 through 203 removed outlier: 6.850A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 261 current: chain 'G' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 284 through 287 current: chain 'G' and resid 315 through 322 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 315 through 322 current: chain 'G' and resid 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 382 through 385 current: chain 'G' and resid 465 through 470 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 11 removed outlier: 7.143A pdb=" N ALA C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP C 37 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 18 through 19 removed outlier: 3.718A pdb=" N VAL C 18 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 82 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP C 81 " --> pdb=" O SER C 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 18 through 23 removed outlier: 3.611A pdb=" N ILE D 21 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER D 63 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.976A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.774A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP H 72 " --> pdb=" O GLN H 77 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER H 70 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 45 through 51 removed outlier: 3.747A pdb=" N THR H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100J through 100O Processing sheet with id=AB7, first strand: chain 'L' and resid 8 through 13 removed outlier: 6.560A pdb=" N ARG L 9 " --> pdb=" O ARG L 103 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N THR L 105 " --> pdb=" O ARG L 9 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 19 through 21 Processing sheet with id=AB9, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.538A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.760A pdb=" N VAL A 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.959A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 86 " --> pdb=" O VAL A 242 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 75 through 76 removed outlier: 7.156A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.539A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AC6, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.563A pdb=" N VAL A 182 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.849A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 287 current: chain 'A' and resid 315 through 322 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 322 current: chain 'A' and resid 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 382 through 385 current: chain 'A' and resid 465 through 470 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AD1, first strand: chain 'F' and resid 10 through 11 removed outlier: 7.143A pdb=" N ALA F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP F 37 " --> pdb=" O PHE F 91 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 18 through 19 removed outlier: 3.718A pdb=" N VAL F 18 " --> pdb=" O LEU F 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 82 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 70 " --> pdb=" O TYR F 79 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP F 81 " --> pdb=" O SER F 68 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 18 through 23 removed outlier: 3.610A pdb=" N ILE I 21 " --> pdb=" O LEU I 73 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR I 71 " --> pdb=" O CYS I 23 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER I 63 " --> pdb=" O THR I 74 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.976A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.774A pdb=" N THR J 21 " --> pdb=" O SER J 7 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU J 78 " --> pdb=" O CYS J 22 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN J 77 " --> pdb=" O ASP J 72 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP J 72 " --> pdb=" O GLN J 77 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER J 70 " --> pdb=" O SER J 79 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 11 through 12 current: chain 'J' and resid 45 through 51 removed outlier: 3.747A pdb=" N THR J 58 " --> pdb=" O TYR J 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100J through 100O Processing sheet with id=AD7, first strand: chain 'K' and resid 8 through 13 removed outlier: 6.560A pdb=" N ARG K 9 " --> pdb=" O ARG K 103 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N THR K 105 " --> pdb=" O ARG K 9 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR K 102 " --> pdb=" O TYR K 86 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 19 through 21 Processing sheet with id=AD9, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.538A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 494 through 499 removed outlier: 5.754A pdb=" N VAL M 36 " --> pdb=" O THR N 606 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR N 606 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 45 through 47 removed outlier: 3.960A pdb=" N ILE M 225 " --> pdb=" O VAL M 245 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL M 242 " --> pdb=" O LEU M 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU M 86 " --> pdb=" O VAL M 242 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 75 through 76 removed outlier: 7.156A pdb=" N CYS M 54 " --> pdb=" O VAL M 75 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 91 through 94 removed outlier: 3.538A pdb=" N GLY M 237 " --> pdb=" O PHE M 93 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 130 through 133 Processing sheet with id=AE6, first strand: chain 'M' and resid 181 through 183 removed outlier: 3.565A pdb=" N VAL M 182 " --> pdb=" O ARG M 192 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 201 through 203 removed outlier: 6.849A pdb=" N THR M 202 " --> pdb=" O TYR M 435 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 259 through 261 current: chain 'M' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 284 through 287 current: chain 'M' and resid 315 through 322 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 315 through 322 current: chain 'M' and resid 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 382 through 385 current: chain 'M' and resid 465 through 470 No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AF1, first strand: chain 'O' and resid 10 through 11 removed outlier: 7.143A pdb=" N ALA O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP O 37 " --> pdb=" O PHE O 91 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE O 34 " --> pdb=" O TRP O 50 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 18 through 19 removed outlier: 3.719A pdb=" N VAL O 18 " --> pdb=" O LEU O 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU O 82 " --> pdb=" O VAL O 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR O 70 " --> pdb=" O TYR O 79 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP O 81 " --> pdb=" O SER O 68 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 18 through 23 removed outlier: 3.610A pdb=" N ILE P 21 " --> pdb=" O LEU P 73 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR P 71 " --> pdb=" O CYS P 23 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER P 63 " --> pdb=" O THR P 74 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 53 through 54 removed outlier: 6.976A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 3 through 7 removed outlier: 3.775A pdb=" N THR Q 21 " --> pdb=" O SER Q 7 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU Q 78 " --> pdb=" O CYS Q 22 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN Q 77 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP Q 72 " --> pdb=" O GLN Q 77 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER Q 70 " --> pdb=" O SER Q 79 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 11 through 12 current: chain 'Q' and resid 45 through 51 removed outlier: 3.748A pdb=" N THR Q 58 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 57 through 59 current: chain 'Q' and resid 100J through 100O Processing sheet with id=AF7, first strand: chain 'R' and resid 8 through 13 removed outlier: 6.560A pdb=" N ARG R 9 " --> pdb=" O ARG R 103 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N THR R 105 " --> pdb=" O ARG R 9 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR R 102 " --> pdb=" O TYR R 86 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 19 through 21 Processing sheet with id=AF9, first strand: chain 'R' and resid 45 through 48 removed outlier: 6.538A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1224 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: 9.25 Time building geometry restraints manager: 8.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8176 1.35 - 1.48: 7230 1.48 - 1.61: 11057 1.61 - 1.74: 0 1.74 - 1.86: 192 Bond restraints: 26655 Sorted by residual: bond pdb=" C1 NAG k 1 " pdb=" O5 NAG k 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.64e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" C1 NAG c 1 " pdb=" O5 NAG c 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" C1 NAG e 1 " pdb=" O5 NAG e 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C1 NAG W 1 " pdb=" O5 NAG W 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.25e+00 ... (remaining 26650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 34792 1.64 - 3.28: 1132 3.28 - 4.92: 184 4.92 - 6.57: 84 6.57 - 8.21: 12 Bond angle restraints: 36204 Sorted by residual: angle pdb=" CA THR A 123 " pdb=" C THR A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 118.44 123.74 -5.30 1.59e+00 3.96e-01 1.11e+01 angle pdb=" CA THR M 123 " pdb=" C THR M 123 " pdb=" N PRO M 124 " ideal model delta sigma weight residual 118.44 123.68 -5.24 1.59e+00 3.96e-01 1.09e+01 angle pdb=" CA THR G 123 " pdb=" C THR G 123 " pdb=" N PRO G 124 " ideal model delta sigma weight residual 118.44 123.68 -5.24 1.59e+00 3.96e-01 1.09e+01 angle pdb=" C ASN R 50 " pdb=" N ASN R 51 " pdb=" CA ASN R 51 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" C ASN K 50 " pdb=" N ASN K 51 " pdb=" CA ASN K 51 " ideal model delta sigma weight residual 121.54 127.67 -6.13 1.91e+00 2.74e-01 1.03e+01 ... (remaining 36199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.57: 16334 21.57 - 43.13: 922 43.13 - 64.70: 135 64.70 - 86.26: 126 86.26 - 107.83: 51 Dihedral angle restraints: 17568 sinusoidal: 8697 harmonic: 8871 Sorted by residual: dihedral pdb=" CB CYS R 23 " pdb=" SG CYS R 23 " pdb=" SG CYS R 88 " pdb=" CB CYS R 88 " ideal model delta sinusoidal sigma weight residual -86.00 -1.12 -84.88 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual -86.00 -1.14 -84.86 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " pdb=" CB CYS K 88 " ideal model delta sinusoidal sigma weight residual -86.00 -1.18 -84.82 1 1.00e+01 1.00e-02 8.73e+01 ... (remaining 17565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.397: 4317 0.397 - 0.794: 21 0.794 - 1.191: 15 1.191 - 1.588: 18 1.588 - 1.985: 3 Chirality restraints: 4374 Sorted by residual: chirality pdb=" C1 MAN p 6 " pdb=" O2 MAN p 5 " pdb=" C2 MAN p 6 " pdb=" O5 MAN p 6 " both_signs ideal model delta sigma weight residual False 2.40 0.41 1.99 2.00e-02 2.50e+03 9.85e+03 chirality pdb=" C1 MAN Z 6 " pdb=" O2 MAN Z 5 " pdb=" C2 MAN Z 6 " pdb=" O5 MAN Z 6 " both_signs ideal model delta sigma weight residual False 2.40 0.42 1.98 2.00e-02 2.50e+03 9.84e+03 chirality pdb=" C1 MAN h 6 " pdb=" O2 MAN h 5 " pdb=" C2 MAN h 6 " pdb=" O5 MAN h 6 " both_signs ideal model delta sigma weight residual False 2.40 0.42 1.98 2.00e-02 2.50e+03 9.81e+03 ... (remaining 4371 not shown) Planarity restraints: 4503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN I 79 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO I 80 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO I 80 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 80 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 79 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO D 80 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 80 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 80 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN P 79 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO P 80 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO P 80 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO P 80 " -0.022 5.00e-02 4.00e+02 ... (remaining 4500 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 8218 2.84 - 3.35: 20373 3.35 - 3.87: 40835 3.87 - 4.38: 44681 4.38 - 4.90: 79689 Nonbonded interactions: 193796 Sorted by model distance: nonbonded pdb=" O GLN Q 5 " pdb=" OG SER Q 23 " model vdw 2.322 3.040 nonbonded pdb=" O GLN H 5 " pdb=" OG SER H 23 " model vdw 2.322 3.040 nonbonded pdb=" O GLN J 5 " pdb=" OG SER J 23 " model vdw 2.322 3.040 nonbonded pdb=" O VAL M 36 " pdb=" OG1 THR N 606 " model vdw 2.335 3.040 nonbonded pdb=" O VAL G 36 " pdb=" OG1 THR B 606 " model vdw 2.345 3.040 ... (remaining 193791 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'P' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'Q' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'o' } ncs_group { reference = chain 'V' selection = chain 'd' selection = chain 'l' } ncs_group { reference = chain 'W' selection = chain 'e' selection = chain 'm' } ncs_group { reference = chain 'X' selection = chain 'f' selection = chain 'n' } ncs_group { reference = chain 'Z' selection = chain 'h' selection = chain 'p' } 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.100 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 59.330 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.006 0.066 26835 Z= 0.277 Angle : 1.705 58.961 36699 Z= 0.620 Chirality : 0.135 1.985 4374 Planarity : 0.004 0.039 4440 Dihedral : 15.805 107.825 11739 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.01 % Allowed : 4.50 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.12), residues: 3021 helix: -4.59 (0.10), residues: 354 sheet: -1.82 (0.16), residues: 777 loop : -2.35 (0.12), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 50 HIS 0.003 0.001 HIS E 564 PHE 0.010 0.001 PHE M 53 TYR 0.009 0.001 TYR D 91 ARG 0.001 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 63) link_NAG-ASN : angle 1.67442 ( 189) link_ALPHA1-6 : bond 0.06482 ( 15) link_ALPHA1-6 : angle 23.08025 ( 45) link_BETA1-4 : bond 0.06501 ( 36) link_BETA1-4 : angle 14.99072 ( 108) link_ALPHA1-2 : bond 0.06528 ( 9) link_ALPHA1-2 : angle 27.86104 ( 27) link_ALPHA1-3 : bond 0.06518 ( 12) link_ALPHA1-3 : angle 22.00461 ( 36) hydrogen bonds : bond 0.28237 ( 480) hydrogen bonds : angle 9.62453 ( 1224) SS BOND : bond 0.00442 ( 45) SS BOND : angle 1.58804 ( 90) covalent geometry : bond 0.00442 (26655) covalent geometry : angle 0.72903 (36204) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 438 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8256 (pt0) cc_final: 0.8002 (pt0) REVERT: B 632 ASP cc_start: 0.8587 (t70) cc_final: 0.8087 (t0) REVERT: C 5 LEU cc_start: 0.8768 (tp) cc_final: 0.8386 (mm) REVERT: C 30 ARG cc_start: 0.7965 (mtt90) cc_final: 0.7594 (mtm-85) REVERT: C 53 LYS cc_start: 0.9295 (ttmt) cc_final: 0.9058 (ttmm) REVERT: C 98 ASP cc_start: 0.8522 (m-30) cc_final: 0.8053 (t0) REVERT: D 77 ASN cc_start: 0.7880 (t0) cc_final: 0.7469 (t0) REVERT: H 3 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7658 (mm-40) REVERT: H 90 TYR cc_start: 0.7983 (m-10) cc_final: 0.7737 (m-10) REVERT: L 79 GLU cc_start: 0.8726 (tp30) cc_final: 0.8259 (tp30) REVERT: E 584 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7673 (mt-10) REVERT: E 632 ASP cc_start: 0.8603 (t70) cc_final: 0.8161 (t0) REVERT: F 5 LEU cc_start: 0.8781 (tp) cc_final: 0.8392 (mm) REVERT: F 13 LYS cc_start: 0.8594 (mttm) cc_final: 0.8111 (mmtt) REVERT: F 31 ASP cc_start: 0.8934 (m-30) cc_final: 0.8714 (m-30) REVERT: F 53 LYS cc_start: 0.9313 (ttmt) cc_final: 0.9042 (ttmm) REVERT: F 98 ASP cc_start: 0.8446 (m-30) cc_final: 0.7997 (t0) REVERT: I 58 VAL cc_start: 0.8818 (t) cc_final: 0.8547 (p) REVERT: I 77 ASN cc_start: 0.7731 (t0) cc_final: 0.7203 (t0) REVERT: K 79 GLU cc_start: 0.8717 (tp30) cc_final: 0.8260 (tp30) REVERT: M 56 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8580 (t) REVERT: M 69 TRP cc_start: 0.7134 (m-90) cc_final: 0.6863 (m-90) REVERT: N 542 ARG cc_start: 0.8563 (ttm170) cc_final: 0.8324 (ttp-170) REVERT: N 568 LEU cc_start: 0.6607 (pp) cc_final: 0.6389 (mt) REVERT: N 632 ASP cc_start: 0.8618 (t70) cc_final: 0.8125 (t0) REVERT: O 5 LEU cc_start: 0.8843 (tp) cc_final: 0.8621 (mm) REVERT: O 30 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7733 (mtt90) REVERT: O 31 ASP cc_start: 0.8908 (m-30) cc_final: 0.8698 (m-30) REVERT: O 98 ASP cc_start: 0.8551 (m-30) cc_final: 0.8229 (t0) REVERT: P 55 GLU cc_start: 0.6771 (tp30) cc_final: 0.6522 (tp30) REVERT: P 77 ASN cc_start: 0.7635 (t0) cc_final: 0.7221 (t0) REVERT: Q 3 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7972 (mm-40) REVERT: Q 46 GLU cc_start: 0.8262 (tt0) cc_final: 0.7902 (tt0) REVERT: Q 86 ASP cc_start: 0.8196 (t0) cc_final: 0.7884 (t0) REVERT: Q 90 TYR cc_start: 0.7907 (m-10) cc_final: 0.7472 (m-10) REVERT: R 42 GLN cc_start: 0.8734 (tp40) cc_final: 0.8098 (mp10) REVERT: R 79 GLU cc_start: 0.8732 (tp30) cc_final: 0.8275 (tp30) outliers start: 27 outliers final: 3 residues processed: 458 average time/residue: 0.4833 time to fit residues: 317.2013 Evaluate side-chains 296 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 292 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain M residue 56 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 235 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 175 optimal weight: 0.5980 chunk 272 optimal weight: 0.3980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 GLN G 315 GLN G 328 GLN G 411 ASN B 590 GLN B 630 GLN C 62 GLN D 69 GLN H 1 GLN H 3 GLN H 31 ASN A 72 HIS A 103 GLN A 315 GLN A 328 GLN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN A 425 ASN E 590 GLN E 630 GLN F 62 GLN I 3 GLN I 69 GLN J 1 GLN J 3 GLN J 31 ASN K 37 GLN M 103 GLN M 315 GLN M 328 GLN M 411 ASN N 590 GLN N 630 GLN O 62 GLN P 3 GLN P 69 GLN Q 1 GLN Q 3 GLN Q 31 ASN R 37 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.085613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.059855 restraints weight = 63117.660| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.51 r_work: 0.2828 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 26835 Z= 0.206 Angle : 0.640 9.408 36699 Z= 0.305 Chirality : 0.046 0.347 4374 Planarity : 0.004 0.065 4440 Dihedral : 11.514 89.564 6091 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.16 % Allowed : 9.86 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.13), residues: 3021 helix: -2.60 (0.20), residues: 384 sheet: -1.58 (0.15), residues: 933 loop : -2.04 (0.13), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 69 HIS 0.002 0.001 HIS A 330 PHE 0.011 0.001 PHE G 53 TYR 0.012 0.001 TYR I 91 ARG 0.007 0.001 ARG J 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 63) link_NAG-ASN : angle 1.81028 ( 189) link_ALPHA1-6 : bond 0.00753 ( 15) link_ALPHA1-6 : angle 2.06742 ( 45) link_BETA1-4 : bond 0.00746 ( 36) link_BETA1-4 : angle 2.33278 ( 108) link_ALPHA1-2 : bond 0.01226 ( 9) link_ALPHA1-2 : angle 1.90991 ( 27) link_ALPHA1-3 : bond 0.01514 ( 12) link_ALPHA1-3 : angle 1.58311 ( 36) hydrogen bonds : bond 0.05291 ( 480) hydrogen bonds : angle 6.46250 ( 1224) SS BOND : bond 0.00367 ( 45) SS BOND : angle 0.89889 ( 90) covalent geometry : bond 0.00472 (26655) covalent geometry : angle 0.60817 (36204) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 290 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 632 ASP cc_start: 0.8997 (t70) cc_final: 0.8481 (t0) REVERT: C 30 ARG cc_start: 0.8268 (mtt90) cc_final: 0.7962 (mtt90) REVERT: C 53 LYS cc_start: 0.9504 (ttmt) cc_final: 0.9197 (ttmm) REVERT: C 82 LYS cc_start: 0.8090 (tttp) cc_final: 0.7880 (ttmm) REVERT: C 98 ASP cc_start: 0.9033 (m-30) cc_final: 0.8223 (t0) REVERT: D 77 ASN cc_start: 0.8244 (t0) cc_final: 0.7841 (t0) REVERT: H 86 ASP cc_start: 0.8507 (t0) cc_final: 0.8227 (t0) REVERT: H 90 TYR cc_start: 0.7897 (m-10) cc_final: 0.7566 (m-10) REVERT: L 66 ASP cc_start: 0.7880 (t0) cc_final: 0.7112 (t0) REVERT: L 79 GLU cc_start: 0.8539 (tp30) cc_final: 0.8177 (tp30) REVERT: E 584 GLU cc_start: 0.8652 (mt-10) cc_final: 0.7968 (mt-10) REVERT: E 632 ASP cc_start: 0.9017 (t70) cc_final: 0.8584 (t0) REVERT: F 53 LYS cc_start: 0.9497 (ttmt) cc_final: 0.9189 (ttmm) REVERT: F 82 LYS cc_start: 0.8096 (tttp) cc_final: 0.7841 (ttmm) REVERT: F 98 ASP cc_start: 0.8967 (m-30) cc_final: 0.8164 (t0) REVERT: I 24 GLN cc_start: 0.8405 (mt0) cc_final: 0.8177 (mp10) REVERT: I 58 VAL cc_start: 0.8762 (t) cc_final: 0.8441 (p) REVERT: I 77 ASN cc_start: 0.7964 (t0) cc_final: 0.7694 (t0) REVERT: J 54 ARG cc_start: 0.8475 (mtt90) cc_final: 0.7935 (mmp80) REVERT: K 79 GLU cc_start: 0.8668 (tp30) cc_final: 0.8077 (tp30) REVERT: M 69 TRP cc_start: 0.7297 (m-90) cc_final: 0.6661 (m-90) REVERT: M 475 MET cc_start: 0.8294 (tpp) cc_final: 0.7915 (mmm) REVERT: N 530 MET cc_start: 0.8777 (mtp) cc_final: 0.8454 (mtp) REVERT: N 542 ARG cc_start: 0.9141 (ttm170) cc_final: 0.8872 (ttp-170) REVERT: N 632 ASP cc_start: 0.9048 (t70) cc_final: 0.8526 (t0) REVERT: O 84 SER cc_start: 0.9227 (m) cc_final: 0.8968 (t) REVERT: O 98 ASP cc_start: 0.9036 (m-30) cc_final: 0.8281 (t0) REVERT: P 55 GLU cc_start: 0.7564 (tp30) cc_final: 0.7109 (tp30) REVERT: P 77 ASN cc_start: 0.7821 (t0) cc_final: 0.7368 (t0) REVERT: Q 46 GLU cc_start: 0.8471 (tt0) cc_final: 0.8117 (tt0) REVERT: Q 86 ASP cc_start: 0.8450 (t0) cc_final: 0.8206 (t0) REVERT: Q 90 TYR cc_start: 0.7790 (m-10) cc_final: 0.7478 (m-10) REVERT: R 42 GLN cc_start: 0.8752 (tp40) cc_final: 0.7965 (mp10) REVERT: R 79 GLU cc_start: 0.8683 (tp30) cc_final: 0.8125 (tp30) outliers start: 31 outliers final: 20 residues processed: 316 average time/residue: 0.4281 time to fit residues: 202.9268 Evaluate side-chains 298 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 278 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 430 ILE Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 168 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 283 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 242 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 GLN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN I 38 GLN P 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.083577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.057342 restraints weight = 63153.246| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.65 r_work: 0.2762 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26835 Z= 0.185 Angle : 0.599 9.728 36699 Z= 0.286 Chirality : 0.045 0.304 4374 Planarity : 0.004 0.052 4440 Dihedral : 9.548 85.244 6087 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.61 % Allowed : 12.52 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.14), residues: 3021 helix: -1.53 (0.25), residues: 381 sheet: -1.14 (0.16), residues: 897 loop : -1.79 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 69 HIS 0.002 0.001 HIS G 85 PHE 0.011 0.001 PHE G 53 TYR 0.010 0.001 TYR D 91 ARG 0.008 0.001 ARG I 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 63) link_NAG-ASN : angle 1.78636 ( 189) link_ALPHA1-6 : bond 0.00778 ( 15) link_ALPHA1-6 : angle 1.62752 ( 45) link_BETA1-4 : bond 0.00570 ( 36) link_BETA1-4 : angle 1.91393 ( 108) link_ALPHA1-2 : bond 0.00655 ( 9) link_ALPHA1-2 : angle 1.96519 ( 27) link_ALPHA1-3 : bond 0.01110 ( 12) link_ALPHA1-3 : angle 1.85878 ( 36) hydrogen bonds : bond 0.03991 ( 480) hydrogen bonds : angle 5.57360 ( 1224) SS BOND : bond 0.00381 ( 45) SS BOND : angle 1.01916 ( 90) covalent geometry : bond 0.00428 (26655) covalent geometry : angle 0.56941 (36204) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 285 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 69 TRP cc_start: 0.6905 (m-90) cc_final: 0.6141 (m-90) REVERT: G 205 CYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7916 (m) REVERT: G 271 MET cc_start: 0.8508 (tpt) cc_final: 0.8265 (mmp) REVERT: B 632 ASP cc_start: 0.9080 (t70) cc_final: 0.8586 (t0) REVERT: C 30 ARG cc_start: 0.8206 (mtt90) cc_final: 0.7919 (mtt90) REVERT: C 53 LYS cc_start: 0.9430 (ttmt) cc_final: 0.9100 (ttmm) REVERT: C 82 LYS cc_start: 0.7950 (tttp) cc_final: 0.7707 (ttmm) REVERT: C 98 ASP cc_start: 0.9010 (m-30) cc_final: 0.8090 (t0) REVERT: D 55 GLU cc_start: 0.8039 (tp30) cc_final: 0.7814 (tp30) REVERT: D 77 ASN cc_start: 0.8377 (t0) cc_final: 0.7989 (t0) REVERT: H 27 ASP cc_start: 0.6534 (t0) cc_final: 0.6333 (t0) REVERT: H 54 ARG cc_start: 0.8572 (mtt90) cc_final: 0.8043 (mmp80) REVERT: H 86 ASP cc_start: 0.8543 (t0) cc_final: 0.8214 (t0) REVERT: H 90 TYR cc_start: 0.7843 (m-10) cc_final: 0.7547 (m-10) REVERT: L 66 ASP cc_start: 0.7912 (t0) cc_final: 0.7170 (t0) REVERT: L 70 ARG cc_start: 0.7312 (mmm160) cc_final: 0.7064 (mmp-170) REVERT: L 79 GLU cc_start: 0.8453 (tp30) cc_final: 0.8110 (tp30) REVERT: A 161 MET cc_start: 0.8553 (tpt) cc_final: 0.8292 (mmm) REVERT: E 584 GLU cc_start: 0.8555 (mt-10) cc_final: 0.7969 (mt-10) REVERT: E 632 ASP cc_start: 0.9002 (t70) cc_final: 0.8584 (t0) REVERT: E 634 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8338 (mt-10) REVERT: F 23 GLU cc_start: 0.7712 (mp0) cc_final: 0.7411 (mp0) REVERT: F 53 LYS cc_start: 0.9427 (ttmt) cc_final: 0.9038 (ttmm) REVERT: F 82 LYS cc_start: 0.7884 (tttp) cc_final: 0.7541 (ttmm) REVERT: F 84 SER cc_start: 0.9314 (m) cc_final: 0.9088 (t) REVERT: F 98 ASP cc_start: 0.8940 (m-30) cc_final: 0.7982 (t0) REVERT: I 24 GLN cc_start: 0.8241 (mt0) cc_final: 0.7956 (mp10) REVERT: I 58 VAL cc_start: 0.8628 (t) cc_final: 0.8292 (p) REVERT: I 77 ASN cc_start: 0.8231 (t0) cc_final: 0.7815 (t0) REVERT: I 103 ARG cc_start: 0.8049 (ptt180) cc_final: 0.7785 (ttp-110) REVERT: J 27 ASP cc_start: 0.6828 (t0) cc_final: 0.6609 (t0) REVERT: J 54 ARG cc_start: 0.8556 (mtt90) cc_final: 0.8042 (mmp80) REVERT: K 66 ASP cc_start: 0.7785 (t0) cc_final: 0.7330 (t0) REVERT: K 79 GLU cc_start: 0.8564 (tp30) cc_final: 0.7989 (tp30) REVERT: M 69 TRP cc_start: 0.7282 (m-90) cc_final: 0.6498 (m-90) REVERT: M 205 CYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7829 (m) REVERT: N 542 ARG cc_start: 0.9176 (ttm170) cc_final: 0.8808 (ttp-170) REVERT: N 632 ASP cc_start: 0.9040 (t70) cc_final: 0.8513 (t0) REVERT: O 30 ARG cc_start: 0.8322 (mtt90) cc_final: 0.7838 (mtt180) REVERT: O 80 MET cc_start: 0.8948 (tmm) cc_final: 0.8542 (tmm) REVERT: O 84 SER cc_start: 0.9309 (m) cc_final: 0.9049 (t) REVERT: O 98 ASP cc_start: 0.8952 (m-30) cc_final: 0.8028 (t0) REVERT: P 55 GLU cc_start: 0.8007 (tp30) cc_final: 0.7576 (tp30) REVERT: P 77 ASN cc_start: 0.8018 (t0) cc_final: 0.7639 (t0) REVERT: P 103 ARG cc_start: 0.8184 (ptt180) cc_final: 0.7895 (ttp-110) REVERT: Q 27 ASP cc_start: 0.7762 (t0) cc_final: 0.7539 (t0) REVERT: Q 32 TYR cc_start: 0.8505 (m-10) cc_final: 0.8178 (m-10) REVERT: Q 46 GLU cc_start: 0.8468 (tt0) cc_final: 0.8254 (tt0) REVERT: Q 86 ASP cc_start: 0.8427 (t0) cc_final: 0.8166 (t0) REVERT: Q 90 TYR cc_start: 0.7700 (m-10) cc_final: 0.7418 (m-10) REVERT: Q 97 ARG cc_start: 0.9024 (tmm-80) cc_final: 0.8274 (ttp80) REVERT: R 70 ARG cc_start: 0.7218 (mmm160) cc_final: 0.6750 (mmp-170) REVERT: R 79 GLU cc_start: 0.8577 (tp30) cc_final: 0.8031 (tp30) outliers start: 43 outliers final: 33 residues processed: 322 average time/residue: 0.4237 time to fit residues: 206.3278 Evaluate side-chains 308 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 273 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 430 ILE Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 31 ASP Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 117 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 290 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 377 ASN A 425 ASN ** M 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.082110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.055905 restraints weight = 63996.676| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.64 r_work: 0.2730 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 26835 Z= 0.213 Angle : 0.619 10.162 36699 Z= 0.295 Chirality : 0.045 0.319 4374 Planarity : 0.004 0.045 4440 Dihedral : 8.632 85.649 6087 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.46 % Favored : 94.47 % Rotamer: Outliers : 2.17 % Allowed : 13.65 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.15), residues: 3021 helix: -0.86 (0.27), residues: 369 sheet: -0.79 (0.17), residues: 918 loop : -1.62 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 69 HIS 0.002 0.001 HIS F 35 PHE 0.013 0.001 PHE D 87 TYR 0.011 0.001 TYR I 91 ARG 0.009 0.001 ARG M 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 63) link_NAG-ASN : angle 1.86451 ( 189) link_ALPHA1-6 : bond 0.00782 ( 15) link_ALPHA1-6 : angle 1.55175 ( 45) link_BETA1-4 : bond 0.00453 ( 36) link_BETA1-4 : angle 1.82272 ( 108) link_ALPHA1-2 : bond 0.00448 ( 9) link_ALPHA1-2 : angle 1.65416 ( 27) link_ALPHA1-3 : bond 0.01076 ( 12) link_ALPHA1-3 : angle 1.72165 ( 36) hydrogen bonds : bond 0.03626 ( 480) hydrogen bonds : angle 5.31425 ( 1224) SS BOND : bond 0.00384 ( 45) SS BOND : angle 0.99979 ( 90) covalent geometry : bond 0.00499 (26655) covalent geometry : angle 0.59158 (36204) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 279 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 69 TRP cc_start: 0.7057 (m-90) cc_final: 0.6441 (m-90) REVERT: G 205 CYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7966 (m) REVERT: G 271 MET cc_start: 0.8472 (tpt) cc_final: 0.8264 (mmp) REVERT: B 632 ASP cc_start: 0.9114 (t70) cc_final: 0.8681 (t0) REVERT: B 634 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8314 (mp0) REVERT: C 30 ARG cc_start: 0.8225 (mtt90) cc_final: 0.7846 (mtt180) REVERT: C 53 LYS cc_start: 0.9430 (ttmt) cc_final: 0.9100 (ttmm) REVERT: C 82 LYS cc_start: 0.7935 (tttp) cc_final: 0.7683 (ttmm) REVERT: C 98 ASP cc_start: 0.8938 (m-30) cc_final: 0.7899 (t0) REVERT: D 55 GLU cc_start: 0.8298 (tp30) cc_final: 0.8045 (tp30) REVERT: D 77 ASN cc_start: 0.8432 (t0) cc_final: 0.7941 (t0) REVERT: D 103 ARG cc_start: 0.8075 (ptt180) cc_final: 0.7817 (ttp-110) REVERT: H 27 ASP cc_start: 0.6670 (t0) cc_final: 0.6413 (t0) REVERT: H 54 ARG cc_start: 0.8559 (mtt90) cc_final: 0.8121 (mmp80) REVERT: H 86 ASP cc_start: 0.8458 (t0) cc_final: 0.8104 (t0) REVERT: H 90 TYR cc_start: 0.7734 (m-10) cc_final: 0.7457 (m-10) REVERT: L 66 ASP cc_start: 0.8123 (t0) cc_final: 0.7794 (t0) REVERT: L 70 ARG cc_start: 0.7278 (mmm160) cc_final: 0.6988 (mmp-170) REVERT: L 79 GLU cc_start: 0.8433 (tp30) cc_final: 0.8097 (tp30) REVERT: A 161 MET cc_start: 0.8473 (tpt) cc_final: 0.8256 (mmm) REVERT: E 584 GLU cc_start: 0.8552 (mt-10) cc_final: 0.7947 (mt-10) REVERT: E 626 MET cc_start: 0.8251 (mtp) cc_final: 0.7788 (mtt) REVERT: E 632 ASP cc_start: 0.9026 (t70) cc_final: 0.8613 (t0) REVERT: E 634 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8277 (mt-10) REVERT: F 23 GLU cc_start: 0.7740 (mp0) cc_final: 0.7429 (mp0) REVERT: F 82 LYS cc_start: 0.7898 (tttp) cc_final: 0.7597 (ttmm) REVERT: F 84 SER cc_start: 0.9373 (m) cc_final: 0.9124 (t) REVERT: F 98 ASP cc_start: 0.8959 (m-30) cc_final: 0.7856 (t0) REVERT: F 100 ASP cc_start: 0.8444 (m-30) cc_final: 0.7794 (p0) REVERT: I 24 GLN cc_start: 0.8177 (mt0) cc_final: 0.7830 (mp10) REVERT: I 55 GLU cc_start: 0.8435 (tp30) cc_final: 0.8222 (tp30) REVERT: I 58 VAL cc_start: 0.8587 (t) cc_final: 0.8244 (p) REVERT: I 77 ASN cc_start: 0.8472 (t0) cc_final: 0.8096 (t0) REVERT: I 103 ARG cc_start: 0.8063 (ptt180) cc_final: 0.7829 (ttp-110) REVERT: J 54 ARG cc_start: 0.8597 (mtt90) cc_final: 0.8102 (mmp80) REVERT: J 86 ASP cc_start: 0.8444 (t0) cc_final: 0.8199 (t0) REVERT: K 26 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8084 (mm-40) REVERT: K 70 ARG cc_start: 0.7150 (mmm160) cc_final: 0.6319 (mmp-170) REVERT: K 79 GLU cc_start: 0.8509 (tp30) cc_final: 0.7955 (tp30) REVERT: K 90 MET cc_start: 0.8989 (tpp) cc_final: 0.8760 (tpp) REVERT: M 69 TRP cc_start: 0.7184 (m-90) cc_final: 0.6464 (m-90) REVERT: M 205 CYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7826 (m) REVERT: M 475 MET cc_start: 0.8484 (mmm) cc_final: 0.8020 (mmm) REVERT: N 542 ARG cc_start: 0.9162 (ttm170) cc_final: 0.8789 (ttp-170) REVERT: N 621 GLU cc_start: 0.9244 (pt0) cc_final: 0.8566 (pp20) REVERT: N 632 ASP cc_start: 0.9048 (t70) cc_final: 0.8524 (t0) REVERT: O 84 SER cc_start: 0.9349 (m) cc_final: 0.9085 (t) REVERT: O 98 ASP cc_start: 0.8934 (m-30) cc_final: 0.7928 (t0) REVERT: P 55 GLU cc_start: 0.8219 (tp30) cc_final: 0.7961 (tp30) REVERT: P 77 ASN cc_start: 0.8047 (t0) cc_final: 0.7700 (t0) REVERT: P 103 ARG cc_start: 0.8146 (ptt180) cc_final: 0.7886 (ttp-110) REVERT: Q 27 ASP cc_start: 0.7680 (t0) cc_final: 0.7408 (t0) REVERT: Q 32 TYR cc_start: 0.8510 (m-10) cc_final: 0.8145 (m-10) REVERT: Q 90 TYR cc_start: 0.7798 (m-10) cc_final: 0.7559 (m-10) REVERT: R 20 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7588 (mpp80) REVERT: R 70 ARG cc_start: 0.7324 (mmm160) cc_final: 0.6979 (mmp-170) REVERT: R 79 GLU cc_start: 0.8547 (tp30) cc_final: 0.8034 (tp30) outliers start: 58 outliers final: 44 residues processed: 330 average time/residue: 0.4213 time to fit residues: 211.9155 Evaluate side-chains 311 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 264 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 430 ILE Chi-restraints excluded: chain N residue 638 TYR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 109 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 chunk 149 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.082341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.056178 restraints weight = 63401.579| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.63 r_work: 0.2738 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26835 Z= 0.176 Angle : 0.597 10.027 36699 Z= 0.284 Chirality : 0.045 0.306 4374 Planarity : 0.004 0.039 4440 Dihedral : 8.320 84.148 6087 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.62 % Allowed : 14.14 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.15), residues: 3021 helix: -0.55 (0.28), residues: 357 sheet: -0.62 (0.17), residues: 918 loop : -1.51 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 69 HIS 0.002 0.001 HIS A 85 PHE 0.011 0.001 PHE D 87 TYR 0.010 0.001 TYR I 91 ARG 0.008 0.000 ARG M 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 63) link_NAG-ASN : angle 1.79166 ( 189) link_ALPHA1-6 : bond 0.00759 ( 15) link_ALPHA1-6 : angle 1.56181 ( 45) link_BETA1-4 : bond 0.00469 ( 36) link_BETA1-4 : angle 1.67479 ( 108) link_ALPHA1-2 : bond 0.00505 ( 9) link_ALPHA1-2 : angle 1.65724 ( 27) link_ALPHA1-3 : bond 0.01046 ( 12) link_ALPHA1-3 : angle 1.58080 ( 36) hydrogen bonds : bond 0.03374 ( 480) hydrogen bonds : angle 5.17041 ( 1224) SS BOND : bond 0.00471 ( 45) SS BOND : angle 0.99466 ( 90) covalent geometry : bond 0.00413 (26655) covalent geometry : angle 0.57124 (36204) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 271 time to evaluate : 3.093 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: G 69 TRP cc_start: 0.7074 (m-90) cc_final: 0.6458 (m-90) REVERT: G 271 MET cc_start: 0.8510 (tpt) cc_final: 0.8233 (mmp) REVERT: G 475 MET cc_start: 0.8269 (mmm) cc_final: 0.8068 (mmm) REVERT: B 632 ASP cc_start: 0.9124 (t70) cc_final: 0.8711 (t0) REVERT: B 634 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8357 (mp0) REVERT: C 30 ARG cc_start: 0.8222 (mtt90) cc_final: 0.7838 (mtt180) REVERT: C 53 LYS cc_start: 0.9438 (ttmt) cc_final: 0.9100 (ttmm) REVERT: C 82 LYS cc_start: 0.7937 (tttp) cc_final: 0.7669 (ttmm) REVERT: C 98 ASP cc_start: 0.8940 (m-30) cc_final: 0.7898 (t0) REVERT: D 5 THR cc_start: 0.7940 (m) cc_final: 0.7581 (p) REVERT: D 55 GLU cc_start: 0.8362 (tp30) cc_final: 0.8129 (tp30) REVERT: D 77 ASN cc_start: 0.8521 (t0) cc_final: 0.8116 (t0) REVERT: D 103 ARG cc_start: 0.8033 (ptt180) cc_final: 0.7771 (ttp-110) REVERT: H 54 ARG cc_start: 0.8553 (mtt90) cc_final: 0.8075 (mmp80) REVERT: H 86 ASP cc_start: 0.8480 (t0) cc_final: 0.8059 (t0) REVERT: H 90 TYR cc_start: 0.7758 (m-10) cc_final: 0.7521 (m-10) REVERT: L 66 ASP cc_start: 0.8064 (t0) cc_final: 0.7353 (t0) REVERT: L 70 ARG cc_start: 0.7294 (mmm160) cc_final: 0.6999 (mmp-170) REVERT: L 79 GLU cc_start: 0.8432 (tp30) cc_final: 0.8077 (tp30) REVERT: A 69 TRP cc_start: 0.6716 (m-90) cc_final: 0.6470 (m-90) REVERT: A 161 MET cc_start: 0.8436 (tpt) cc_final: 0.8231 (mmm) REVERT: E 584 GLU cc_start: 0.8547 (mt-10) cc_final: 0.7925 (mt-10) REVERT: E 632 ASP cc_start: 0.9034 (t70) cc_final: 0.8624 (t0) REVERT: F 23 GLU cc_start: 0.7781 (mp0) cc_final: 0.7443 (mp0) REVERT: F 82 LYS cc_start: 0.7904 (tttp) cc_final: 0.7598 (ttmm) REVERT: F 84 SER cc_start: 0.9354 (m) cc_final: 0.9104 (t) REVERT: F 98 ASP cc_start: 0.8952 (m-30) cc_final: 0.7817 (t0) REVERT: F 100 ASP cc_start: 0.8360 (m-30) cc_final: 0.7814 (p0) REVERT: I 24 GLN cc_start: 0.8131 (mt0) cc_final: 0.7769 (mp10) REVERT: I 55 GLU cc_start: 0.8461 (tp30) cc_final: 0.8235 (tp30) REVERT: I 58 VAL cc_start: 0.8508 (t) cc_final: 0.8158 (p) REVERT: I 77 ASN cc_start: 0.8521 (t0) cc_final: 0.8227 (t0) REVERT: I 103 ARG cc_start: 0.8104 (ptt180) cc_final: 0.7867 (ttp-110) REVERT: J 54 ARG cc_start: 0.8626 (mtt90) cc_final: 0.8101 (mmp80) REVERT: J 86 ASP cc_start: 0.8446 (t0) cc_final: 0.8188 (t0) REVERT: K 26 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8151 (mm-40) REVERT: K 70 ARG cc_start: 0.7087 (mmm160) cc_final: 0.6507 (mmp-170) REVERT: K 79 GLU cc_start: 0.8475 (tp30) cc_final: 0.7950 (tp30) REVERT: K 90 MET cc_start: 0.8990 (tpp) cc_final: 0.8775 (tpp) REVERT: M 69 TRP cc_start: 0.7241 (m-90) cc_final: 0.6490 (m-90) REVERT: M 205 CYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7834 (m) REVERT: M 475 MET cc_start: 0.8510 (mmm) cc_final: 0.8065 (mmm) REVERT: N 542 ARG cc_start: 0.9153 (ttm170) cc_final: 0.8772 (ttp-170) REVERT: N 621 GLU cc_start: 0.9246 (pt0) cc_final: 0.8481 (pp20) REVERT: N 632 ASP cc_start: 0.9035 (t70) cc_final: 0.8507 (t0) REVERT: O 84 SER cc_start: 0.9355 (m) cc_final: 0.9090 (t) REVERT: O 98 ASP cc_start: 0.8912 (m-30) cc_final: 0.7880 (t0) REVERT: P 5 THR cc_start: 0.7998 (m) cc_final: 0.7603 (p) REVERT: P 55 GLU cc_start: 0.8303 (tp30) cc_final: 0.8048 (tp30) REVERT: P 77 ASN cc_start: 0.8292 (t0) cc_final: 0.7991 (t0) REVERT: P 103 ARG cc_start: 0.8145 (ptt180) cc_final: 0.7878 (ttp-110) REVERT: Q 27 ASP cc_start: 0.7690 (t0) cc_final: 0.7472 (t0) REVERT: Q 32 TYR cc_start: 0.8456 (m-10) cc_final: 0.8077 (m-10) REVERT: R 20 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.7585 (mpp80) REVERT: R 70 ARG cc_start: 0.7304 (mmm160) cc_final: 0.6943 (mmp-170) REVERT: R 79 GLU cc_start: 0.8535 (tp30) cc_final: 0.8036 (tp30) outliers start: 70 outliers final: 54 residues processed: 333 average time/residue: 0.4164 time to fit residues: 210.7012 Evaluate side-chains 319 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 263 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 430 ILE Chi-restraints excluded: chain M residue 488 VAL Chi-restraints excluded: chain N residue 638 TYR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 241 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 GLN ** M 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.082197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.056088 restraints weight = 63187.720| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.62 r_work: 0.2738 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26835 Z= 0.165 Angle : 0.588 9.994 36699 Z= 0.280 Chirality : 0.044 0.303 4374 Planarity : 0.003 0.036 4440 Dihedral : 8.029 83.238 6087 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.66 % Allowed : 14.66 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.15), residues: 3021 helix: -0.47 (0.27), residues: 381 sheet: -0.44 (0.17), residues: 918 loop : -1.50 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 69 HIS 0.002 0.001 HIS A 85 PHE 0.012 0.001 PHE F 73 TYR 0.010 0.001 TYR I 91 ARG 0.009 0.000 ARG M 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 63) link_NAG-ASN : angle 1.74608 ( 189) link_ALPHA1-6 : bond 0.00760 ( 15) link_ALPHA1-6 : angle 1.51304 ( 45) link_BETA1-4 : bond 0.00459 ( 36) link_BETA1-4 : angle 1.61730 ( 108) link_ALPHA1-2 : bond 0.00503 ( 9) link_ALPHA1-2 : angle 1.59471 ( 27) link_ALPHA1-3 : bond 0.01031 ( 12) link_ALPHA1-3 : angle 1.48581 ( 36) hydrogen bonds : bond 0.03155 ( 480) hydrogen bonds : angle 5.00469 ( 1224) SS BOND : bond 0.00342 ( 45) SS BOND : angle 0.90969 ( 90) covalent geometry : bond 0.00388 (26655) covalent geometry : angle 0.56372 (36204) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 279 time to evaluate : 3.056 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: G 69 TRP cc_start: 0.7041 (m-90) cc_final: 0.6514 (m-90) REVERT: G 271 MET cc_start: 0.8524 (tpt) cc_final: 0.8229 (mmp) REVERT: B 632 ASP cc_start: 0.9084 (t70) cc_final: 0.8659 (t0) REVERT: B 634 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8414 (mp0) REVERT: C 5 LEU cc_start: 0.8413 (tp) cc_final: 0.8089 (tp) REVERT: C 23 GLU cc_start: 0.7668 (mp0) cc_final: 0.7318 (mp0) REVERT: C 30 ARG cc_start: 0.8225 (mtt90) cc_final: 0.7837 (mtt180) REVERT: C 53 LYS cc_start: 0.9433 (ttmt) cc_final: 0.9099 (ttmm) REVERT: C 82 LYS cc_start: 0.7923 (tttp) cc_final: 0.7660 (ttmm) REVERT: C 98 ASP cc_start: 0.8937 (m-30) cc_final: 0.7914 (t0) REVERT: D 5 THR cc_start: 0.7888 (m) cc_final: 0.7477 (p) REVERT: D 55 GLU cc_start: 0.8392 (tp30) cc_final: 0.8071 (tp30) REVERT: D 77 ASN cc_start: 0.8566 (t0) cc_final: 0.8220 (t0) REVERT: D 103 ARG cc_start: 0.7998 (ptt180) cc_final: 0.7732 (ttp-110) REVERT: H 54 ARG cc_start: 0.8608 (mtt90) cc_final: 0.8082 (mmp80) REVERT: H 86 ASP cc_start: 0.8454 (t0) cc_final: 0.8081 (t0) REVERT: H 90 TYR cc_start: 0.7759 (m-10) cc_final: 0.7483 (m-10) REVERT: H 100 MET cc_start: 0.8245 (mmt) cc_final: 0.7628 (mmt) REVERT: L 66 ASP cc_start: 0.8129 (t0) cc_final: 0.7419 (t0) REVERT: L 70 ARG cc_start: 0.7277 (mmm160) cc_final: 0.7047 (mmp-170) REVERT: L 79 GLU cc_start: 0.8425 (tp30) cc_final: 0.8026 (tp30) REVERT: A 69 TRP cc_start: 0.6823 (m-90) cc_final: 0.6580 (m-90) REVERT: E 626 MET cc_start: 0.8296 (mtp) cc_final: 0.8032 (mtt) REVERT: E 632 ASP cc_start: 0.8987 (t70) cc_final: 0.8575 (t0) REVERT: E 634 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8505 (mt-10) REVERT: F 23 GLU cc_start: 0.7785 (mp0) cc_final: 0.7453 (mp0) REVERT: F 82 LYS cc_start: 0.7936 (tttp) cc_final: 0.7618 (ttmm) REVERT: F 84 SER cc_start: 0.9369 (m) cc_final: 0.9117 (t) REVERT: F 98 ASP cc_start: 0.8942 (m-30) cc_final: 0.7760 (t0) REVERT: F 100 ASP cc_start: 0.8363 (m-30) cc_final: 0.7863 (p0) REVERT: I 1 ASP cc_start: 0.7849 (p0) cc_final: 0.7553 (p0) REVERT: I 24 GLN cc_start: 0.8097 (mt0) cc_final: 0.7695 (mp10) REVERT: I 55 GLU cc_start: 0.8487 (tp30) cc_final: 0.8271 (tp30) REVERT: I 58 VAL cc_start: 0.8491 (t) cc_final: 0.8134 (p) REVERT: I 77 ASN cc_start: 0.8507 (t0) cc_final: 0.8196 (t0) REVERT: I 103 ARG cc_start: 0.8140 (ptt180) cc_final: 0.7888 (ttp-110) REVERT: J 54 ARG cc_start: 0.8665 (mtt90) cc_final: 0.8109 (mmp80) REVERT: J 86 ASP cc_start: 0.8427 (t0) cc_final: 0.8138 (t0) REVERT: K 79 GLU cc_start: 0.8470 (tp30) cc_final: 0.7933 (tp30) REVERT: K 90 MET cc_start: 0.8999 (tpp) cc_final: 0.8745 (tpp) REVERT: M 69 TRP cc_start: 0.7123 (m-90) cc_final: 0.6439 (m-90) REVERT: M 475 MET cc_start: 0.8626 (mmm) cc_final: 0.8164 (mmm) REVERT: N 542 ARG cc_start: 0.9150 (ttm170) cc_final: 0.8733 (ttp-170) REVERT: N 621 GLU cc_start: 0.9258 (pt0) cc_final: 0.8506 (pp20) REVERT: N 632 ASP cc_start: 0.8986 (t70) cc_final: 0.8437 (t0) REVERT: O 30 ARG cc_start: 0.8284 (mtt90) cc_final: 0.7897 (mtt90) REVERT: O 84 SER cc_start: 0.9364 (m) cc_final: 0.9090 (t) REVERT: O 98 ASP cc_start: 0.8904 (m-30) cc_final: 0.7859 (t0) REVERT: P 5 THR cc_start: 0.7998 (m) cc_final: 0.7574 (p) REVERT: P 55 GLU cc_start: 0.8329 (tp30) cc_final: 0.8108 (tp30) REVERT: P 77 ASN cc_start: 0.8305 (t0) cc_final: 0.7905 (t0) REVERT: P 103 ARG cc_start: 0.8149 (ptt180) cc_final: 0.7882 (ttp-110) REVERT: Q 32 TYR cc_start: 0.8438 (m-10) cc_final: 0.8080 (m-10) REVERT: Q 54 ARG cc_start: 0.8335 (ptp90) cc_final: 0.8089 (mmp80) REVERT: Q 86 ASP cc_start: 0.8566 (t0) cc_final: 0.8339 (t0) REVERT: R 20 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7580 (mpp80) REVERT: R 79 GLU cc_start: 0.8525 (tp30) cc_final: 0.8012 (tp30) outliers start: 71 outliers final: 57 residues processed: 342 average time/residue: 0.4290 time to fit residues: 222.4768 Evaluate side-chains 323 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 265 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 430 ILE Chi-restraints excluded: chain M residue 488 VAL Chi-restraints excluded: chain N residue 638 TYR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 168 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 244 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN M 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.082430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.056361 restraints weight = 63379.031| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.62 r_work: 0.2744 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26835 Z= 0.146 Angle : 0.584 10.842 36699 Z= 0.278 Chirality : 0.044 0.296 4374 Planarity : 0.003 0.040 4440 Dihedral : 7.819 82.289 6087 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.51 % Allowed : 15.45 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.15), residues: 3021 helix: -0.21 (0.28), residues: 381 sheet: -0.32 (0.17), residues: 918 loop : -1.45 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 69 HIS 0.002 0.001 HIS C 71A PHE 0.009 0.001 PHE I 87 TYR 0.010 0.001 TYR I 91 ARG 0.010 0.000 ARG M 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 63) link_NAG-ASN : angle 1.70271 ( 189) link_ALPHA1-6 : bond 0.00752 ( 15) link_ALPHA1-6 : angle 1.49017 ( 45) link_BETA1-4 : bond 0.00464 ( 36) link_BETA1-4 : angle 1.56201 ( 108) link_ALPHA1-2 : bond 0.00516 ( 9) link_ALPHA1-2 : angle 1.56068 ( 27) link_ALPHA1-3 : bond 0.01026 ( 12) link_ALPHA1-3 : angle 1.44852 ( 36) hydrogen bonds : bond 0.02979 ( 480) hydrogen bonds : angle 4.87274 ( 1224) SS BOND : bond 0.00375 ( 45) SS BOND : angle 0.94028 ( 90) covalent geometry : bond 0.00344 (26655) covalent geometry : angle 0.56033 (36204) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 266 time to evaluate : 3.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 69 TRP cc_start: 0.7024 (m-90) cc_final: 0.6545 (m-90) REVERT: G 271 MET cc_start: 0.8532 (tpt) cc_final: 0.8235 (mmp) REVERT: B 632 ASP cc_start: 0.9087 (t70) cc_final: 0.8617 (t0) REVERT: C 5 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8111 (tp) REVERT: C 23 GLU cc_start: 0.7682 (mp0) cc_final: 0.7316 (mp0) REVERT: C 30 ARG cc_start: 0.8211 (mtt90) cc_final: 0.7816 (mtt180) REVERT: C 53 LYS cc_start: 0.9448 (ttmt) cc_final: 0.9107 (ttmm) REVERT: C 82 LYS cc_start: 0.7942 (tttp) cc_final: 0.7358 (tppt) REVERT: C 98 ASP cc_start: 0.8948 (m-30) cc_final: 0.7896 (t0) REVERT: D 5 THR cc_start: 0.7816 (m) cc_final: 0.7419 (p) REVERT: D 55 GLU cc_start: 0.8462 (tp30) cc_final: 0.8152 (tp30) REVERT: D 77 ASN cc_start: 0.8612 (t0) cc_final: 0.8358 (t0) REVERT: D 103 ARG cc_start: 0.7995 (ptt180) cc_final: 0.7726 (ttp-110) REVERT: H 86 ASP cc_start: 0.8449 (t0) cc_final: 0.8141 (t0) REVERT: H 90 TYR cc_start: 0.7795 (m-10) cc_final: 0.7574 (m-10) REVERT: L 66 ASP cc_start: 0.8197 (t0) cc_final: 0.7487 (t0) REVERT: L 70 ARG cc_start: 0.7296 (mmm160) cc_final: 0.7072 (mmp-170) REVERT: L 79 GLU cc_start: 0.8432 (tp30) cc_final: 0.8027 (tp30) REVERT: A 69 TRP cc_start: 0.6876 (m-90) cc_final: 0.6619 (m-90) REVERT: E 626 MET cc_start: 0.8400 (mtp) cc_final: 0.7912 (mtt) REVERT: E 632 ASP cc_start: 0.8953 (t70) cc_final: 0.8532 (t0) REVERT: E 634 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8431 (mt-10) REVERT: F 23 GLU cc_start: 0.7789 (mp0) cc_final: 0.7451 (mp0) REVERT: F 82 LYS cc_start: 0.7960 (tttp) cc_final: 0.7643 (ttmm) REVERT: F 84 SER cc_start: 0.9365 (m) cc_final: 0.9104 (t) REVERT: F 98 ASP cc_start: 0.8943 (m-30) cc_final: 0.7797 (t0) REVERT: F 100 ASP cc_start: 0.8298 (m-30) cc_final: 0.7845 (p0) REVERT: I 1 ASP cc_start: 0.7903 (p0) cc_final: 0.7635 (p0) REVERT: I 24 GLN cc_start: 0.8069 (mt0) cc_final: 0.7703 (mp10) REVERT: I 58 VAL cc_start: 0.8451 (t) cc_final: 0.8109 (p) REVERT: I 103 ARG cc_start: 0.8117 (ptt180) cc_final: 0.7871 (ttp-110) REVERT: J 54 ARG cc_start: 0.8679 (mtt90) cc_final: 0.8122 (mmp80) REVERT: J 86 ASP cc_start: 0.8425 (t0) cc_final: 0.8135 (t0) REVERT: K 79 GLU cc_start: 0.8475 (tp30) cc_final: 0.7929 (tp30) REVERT: K 90 MET cc_start: 0.9035 (tpp) cc_final: 0.8770 (tpp) REVERT: M 69 TRP cc_start: 0.7058 (m-90) cc_final: 0.6375 (m-90) REVERT: M 205 CYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7799 (m) REVERT: M 475 MET cc_start: 0.8658 (mmm) cc_final: 0.8143 (mmm) REVERT: M 504 ARG cc_start: 0.8378 (mmm160) cc_final: 0.8066 (mmm160) REVERT: N 542 ARG cc_start: 0.9130 (ttm170) cc_final: 0.8734 (ttp-170) REVERT: N 621 GLU cc_start: 0.9236 (pt0) cc_final: 0.8562 (pp20) REVERT: N 632 ASP cc_start: 0.8969 (t70) cc_final: 0.8416 (t0) REVERT: O 30 ARG cc_start: 0.8284 (mtt90) cc_final: 0.7906 (mtt90) REVERT: O 84 SER cc_start: 0.9366 (m) cc_final: 0.9086 (t) REVERT: O 100 ASP cc_start: 0.8372 (m-30) cc_final: 0.7815 (p0) REVERT: P 5 THR cc_start: 0.7867 (m) cc_final: 0.7518 (p) REVERT: P 55 GLU cc_start: 0.8337 (tp30) cc_final: 0.8007 (tp30) REVERT: P 58 VAL cc_start: 0.8444 (t) cc_final: 0.8037 (p) REVERT: P 77 ASN cc_start: 0.8454 (t0) cc_final: 0.8185 (t0) REVERT: P 103 ARG cc_start: 0.8135 (ptt180) cc_final: 0.7871 (ttp-110) REVERT: Q 27 ASP cc_start: 0.5590 (t0) cc_final: 0.5088 (t0) REVERT: Q 32 TYR cc_start: 0.8645 (m-10) cc_final: 0.8222 (m-10) REVERT: Q 54 ARG cc_start: 0.8340 (ptp90) cc_final: 0.8102 (mmp80) REVERT: Q 86 ASP cc_start: 0.8665 (t0) cc_final: 0.8382 (t0) REVERT: R 20 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7574 (mpp80) REVERT: R 70 ARG cc_start: 0.7510 (mmm160) cc_final: 0.7161 (mmp-170) REVERT: R 79 GLU cc_start: 0.8532 (tp30) cc_final: 0.8014 (tp30) outliers start: 67 outliers final: 54 residues processed: 326 average time/residue: 0.4192 time to fit residues: 207.7681 Evaluate side-chains 315 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 258 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 425 ASN Chi-restraints excluded: chain M residue 430 ILE Chi-restraints excluded: chain M residue 488 VAL Chi-restraints excluded: chain N residue 638 TYR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 46 optimal weight: 0.9990 chunk 123 optimal weight: 0.0070 chunk 299 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 chunk 179 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 245 optimal weight: 0.6980 chunk 277 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 overall best weight: 0.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** M 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.083044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.057002 restraints weight = 63188.710| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.62 r_work: 0.2759 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26835 Z= 0.117 Angle : 0.570 9.898 36699 Z= 0.272 Chirality : 0.043 0.283 4374 Planarity : 0.003 0.048 4440 Dihedral : 7.609 81.323 6087 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.62 % Allowed : 15.67 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.15), residues: 3021 helix: 0.01 (0.29), residues: 381 sheet: -0.18 (0.18), residues: 912 loop : -1.40 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 69 HIS 0.002 0.000 HIS G 374 PHE 0.008 0.001 PHE G 53 TYR 0.009 0.001 TYR G 484 ARG 0.012 0.000 ARG I 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 63) link_NAG-ASN : angle 1.63305 ( 189) link_ALPHA1-6 : bond 0.00753 ( 15) link_ALPHA1-6 : angle 1.46012 ( 45) link_BETA1-4 : bond 0.00479 ( 36) link_BETA1-4 : angle 1.50293 ( 108) link_ALPHA1-2 : bond 0.00571 ( 9) link_ALPHA1-2 : angle 1.52560 ( 27) link_ALPHA1-3 : bond 0.01050 ( 12) link_ALPHA1-3 : angle 1.43121 ( 36) hydrogen bonds : bond 0.02751 ( 480) hydrogen bonds : angle 4.75680 ( 1224) SS BOND : bond 0.00343 ( 45) SS BOND : angle 0.84121 ( 90) covalent geometry : bond 0.00274 (26655) covalent geometry : angle 0.54822 (36204) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 271 time to evaluate : 2.932 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: G 69 TRP cc_start: 0.6947 (m-90) cc_final: 0.6562 (m-90) REVERT: G 271 MET cc_start: 0.8543 (tpt) cc_final: 0.8214 (mmp) REVERT: B 632 ASP cc_start: 0.9036 (t70) cc_final: 0.8542 (t0) REVERT: C 5 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8133 (tp) REVERT: C 23 GLU cc_start: 0.7655 (mp0) cc_final: 0.7311 (mp0) REVERT: C 30 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7741 (mtt180) REVERT: C 53 LYS cc_start: 0.9448 (ttmt) cc_final: 0.9117 (ttmm) REVERT: C 82 LYS cc_start: 0.7966 (tttp) cc_final: 0.7706 (ttmm) REVERT: C 98 ASP cc_start: 0.8946 (m-30) cc_final: 0.7907 (t0) REVERT: D 5 THR cc_start: 0.7711 (m) cc_final: 0.7354 (p) REVERT: D 55 GLU cc_start: 0.8467 (tp30) cc_final: 0.8103 (tp30) REVERT: D 58 VAL cc_start: 0.8460 (t) cc_final: 0.8118 (p) REVERT: D 60 SER cc_start: 0.8470 (t) cc_final: 0.8201 (m) REVERT: D 77 ASN cc_start: 0.8613 (t0) cc_final: 0.8367 (t0) REVERT: D 103 ARG cc_start: 0.8026 (ptt180) cc_final: 0.7762 (ttp-110) REVERT: H 86 ASP cc_start: 0.8436 (t0) cc_final: 0.8112 (t0) REVERT: H 90 TYR cc_start: 0.7743 (m-10) cc_final: 0.7489 (m-10) REVERT: L 66 ASP cc_start: 0.8179 (t0) cc_final: 0.7423 (t0) REVERT: L 70 ARG cc_start: 0.7267 (mmm160) cc_final: 0.7059 (mmp-170) REVERT: L 79 GLU cc_start: 0.8408 (tp30) cc_final: 0.8021 (tp30) REVERT: A 69 TRP cc_start: 0.6850 (m-90) cc_final: 0.6569 (m-90) REVERT: A 475 MET cc_start: 0.8445 (mmm) cc_final: 0.8169 (mmt) REVERT: A 502 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8246 (tptp) REVERT: E 626 MET cc_start: 0.8386 (mtp) cc_final: 0.7837 (mtt) REVERT: E 632 ASP cc_start: 0.8915 (t70) cc_final: 0.8501 (t0) REVERT: E 634 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8433 (mt-10) REVERT: F 5 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8181 (mm) REVERT: F 23 GLU cc_start: 0.7781 (mp0) cc_final: 0.7424 (mp0) REVERT: F 82 LYS cc_start: 0.7959 (tttp) cc_final: 0.7650 (ttmm) REVERT: F 98 ASP cc_start: 0.8938 (m-30) cc_final: 0.7784 (t0) REVERT: F 100 ASP cc_start: 0.8254 (m-30) cc_final: 0.7843 (p0) REVERT: I 1 ASP cc_start: 0.7884 (p0) cc_final: 0.7626 (p0) REVERT: I 5 THR cc_start: 0.8246 (m) cc_final: 0.7543 (p) REVERT: I 24 GLN cc_start: 0.8111 (mt0) cc_final: 0.7668 (mp10) REVERT: I 55 GLU cc_start: 0.8392 (tp30) cc_final: 0.8144 (tp30) REVERT: I 58 VAL cc_start: 0.8493 (t) cc_final: 0.8124 (p) REVERT: I 103 ARG cc_start: 0.8110 (ptt180) cc_final: 0.7851 (ttp-110) REVERT: J 54 ARG cc_start: 0.8742 (mtt90) cc_final: 0.8142 (mmp80) REVERT: J 86 ASP cc_start: 0.8424 (t0) cc_final: 0.8127 (t0) REVERT: K 70 ARG cc_start: 0.6864 (mmp-170) cc_final: 0.6538 (mmp-170) REVERT: K 79 GLU cc_start: 0.8473 (tp30) cc_final: 0.7928 (tp30) REVERT: K 90 MET cc_start: 0.9026 (tpp) cc_final: 0.8728 (tpp) REVERT: M 69 TRP cc_start: 0.6986 (m-90) cc_final: 0.6382 (m-90) REVERT: M 475 MET cc_start: 0.8629 (mmm) cc_final: 0.8173 (mmm) REVERT: M 504 ARG cc_start: 0.8348 (mmm160) cc_final: 0.8065 (mmm160) REVERT: N 542 ARG cc_start: 0.9119 (ttm170) cc_final: 0.8722 (ttp-170) REVERT: N 621 GLU cc_start: 0.9242 (pt0) cc_final: 0.8570 (pp20) REVERT: N 632 ASP cc_start: 0.8926 (t70) cc_final: 0.8361 (t0) REVERT: O 30 ARG cc_start: 0.8254 (mtt90) cc_final: 0.7885 (mtt90) REVERT: O 84 SER cc_start: 0.9360 (m) cc_final: 0.9068 (t) REVERT: O 100 ASP cc_start: 0.8320 (m-30) cc_final: 0.7791 (p0) REVERT: P 5 THR cc_start: 0.7799 (m) cc_final: 0.7435 (p) REVERT: P 55 GLU cc_start: 0.8360 (tp30) cc_final: 0.8053 (tp30) REVERT: P 58 VAL cc_start: 0.8453 (t) cc_final: 0.8047 (p) REVERT: P 77 ASN cc_start: 0.8447 (t0) cc_final: 0.8189 (t0) REVERT: P 103 ARG cc_start: 0.8137 (ptt180) cc_final: 0.7867 (ttp-110) REVERT: Q 27 ASP cc_start: 0.5531 (t0) cc_final: 0.5050 (t0) REVERT: Q 32 TYR cc_start: 0.8637 (m-10) cc_final: 0.8213 (m-10) REVERT: Q 54 ARG cc_start: 0.8389 (ptp90) cc_final: 0.8086 (mmp80) REVERT: Q 86 ASP cc_start: 0.8669 (t0) cc_final: 0.8345 (t0) REVERT: R 20 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7567 (mpp80) REVERT: R 26 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7908 (mm-40) REVERT: R 79 GLU cc_start: 0.8521 (tp30) cc_final: 0.8003 (tp30) outliers start: 70 outliers final: 53 residues processed: 333 average time/residue: 0.4144 time to fit residues: 209.5930 Evaluate side-chains 319 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 262 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 488 VAL Chi-restraints excluded: chain N residue 638 TYR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 31 ASP Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 177 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN M 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.080785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.054733 restraints weight = 64231.951| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.60 r_work: 0.2706 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 26835 Z= 0.245 Angle : 0.653 10.339 36699 Z= 0.312 Chirality : 0.045 0.331 4374 Planarity : 0.004 0.036 4440 Dihedral : 7.918 83.094 6087 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.02 % Favored : 93.88 % Rotamer: Outliers : 2.59 % Allowed : 16.05 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.15), residues: 3021 helix: -0.12 (0.28), residues: 384 sheet: -0.39 (0.17), residues: 969 loop : -1.44 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 69 HIS 0.003 0.001 HIS G 85 PHE 0.014 0.002 PHE I 87 TYR 0.013 0.001 TYR D 91 ARG 0.010 0.001 ARG I 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 63) link_NAG-ASN : angle 1.82133 ( 189) link_ALPHA1-6 : bond 0.00682 ( 15) link_ALPHA1-6 : angle 1.46092 ( 45) link_BETA1-4 : bond 0.00463 ( 36) link_BETA1-4 : angle 1.68986 ( 108) link_ALPHA1-2 : bond 0.00421 ( 9) link_ALPHA1-2 : angle 1.71202 ( 27) link_ALPHA1-3 : bond 0.00901 ( 12) link_ALPHA1-3 : angle 1.44503 ( 36) hydrogen bonds : bond 0.03436 ( 480) hydrogen bonds : angle 4.85864 ( 1224) SS BOND : bond 0.00436 ( 45) SS BOND : angle 1.10893 ( 90) covalent geometry : bond 0.00574 (26655) covalent geometry : angle 0.62987 (36204) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 256 time to evaluate : 2.808 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: G 69 TRP cc_start: 0.7034 (m-90) cc_final: 0.6493 (m-90) REVERT: G 271 MET cc_start: 0.8547 (tpt) cc_final: 0.8257 (mmp) REVERT: G 475 MET cc_start: 0.8563 (mmm) cc_final: 0.8273 (mmm) REVERT: B 632 ASP cc_start: 0.9170 (t70) cc_final: 0.8711 (t0) REVERT: C 5 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8043 (tp) REVERT: C 23 GLU cc_start: 0.7745 (mp0) cc_final: 0.7329 (mp0) REVERT: C 30 ARG cc_start: 0.8237 (mtt90) cc_final: 0.7826 (mtt180) REVERT: C 53 LYS cc_start: 0.9453 (ttmt) cc_final: 0.9099 (ttmm) REVERT: C 82 LYS cc_start: 0.7967 (tttp) cc_final: 0.7389 (tppt) REVERT: C 98 ASP cc_start: 0.8934 (m-30) cc_final: 0.7850 (t0) REVERT: D 5 THR cc_start: 0.7938 (m) cc_final: 0.7519 (p) REVERT: D 55 GLU cc_start: 0.8506 (tp30) cc_final: 0.8081 (tp30) REVERT: D 58 VAL cc_start: 0.8456 (t) cc_final: 0.8126 (p) REVERT: D 77 ASN cc_start: 0.8668 (t0) cc_final: 0.8406 (t0) REVERT: D 103 ARG cc_start: 0.8048 (ptt180) cc_final: 0.7818 (ttp-110) REVERT: H 86 ASP cc_start: 0.8410 (t0) cc_final: 0.8133 (t0) REVERT: H 100 MET cc_start: 0.8322 (mmt) cc_final: 0.7729 (mmt) REVERT: L 70 ARG cc_start: 0.7336 (mmm160) cc_final: 0.7094 (mmp-170) REVERT: L 79 GLU cc_start: 0.8335 (tp30) cc_final: 0.7985 (tp30) REVERT: A 69 TRP cc_start: 0.6957 (m-90) cc_final: 0.6679 (m-90) REVERT: A 502 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8312 (tptp) REVERT: E 626 MET cc_start: 0.8350 (mtp) cc_final: 0.7860 (mtt) REVERT: E 632 ASP cc_start: 0.8985 (t70) cc_final: 0.8571 (t0) REVERT: E 634 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8433 (mt-10) REVERT: F 5 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8106 (mm) REVERT: F 23 GLU cc_start: 0.7857 (mp0) cc_final: 0.7486 (mp0) REVERT: F 82 LYS cc_start: 0.7971 (tttp) cc_final: 0.7626 (ttmm) REVERT: F 84 SER cc_start: 0.9399 (m) cc_final: 0.9139 (t) REVERT: F 98 ASP cc_start: 0.8926 (m-30) cc_final: 0.7745 (t0) REVERT: F 100 ASP cc_start: 0.8388 (m-30) cc_final: 0.7914 (p0) REVERT: I 1 ASP cc_start: 0.8101 (p0) cc_final: 0.7827 (p0) REVERT: I 5 THR cc_start: 0.8267 (m) cc_final: 0.7605 (p) REVERT: I 24 GLN cc_start: 0.8232 (mt0) cc_final: 0.7832 (mp10) REVERT: I 58 VAL cc_start: 0.8433 (t) cc_final: 0.8062 (p) REVERT: I 103 ARG cc_start: 0.8112 (ptt180) cc_final: 0.7885 (ttp-110) REVERT: J 54 ARG cc_start: 0.8768 (mtt90) cc_final: 0.8173 (mmp80) REVERT: J 86 ASP cc_start: 0.8408 (t0) cc_final: 0.8141 (t0) REVERT: K 79 GLU cc_start: 0.8369 (tp30) cc_final: 0.7835 (tp30) REVERT: K 90 MET cc_start: 0.9011 (tpp) cc_final: 0.8795 (tpp) REVERT: M 69 TRP cc_start: 0.7076 (m-90) cc_final: 0.6376 (m-90) REVERT: M 205 CYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7795 (m) REVERT: N 542 ARG cc_start: 0.9191 (ttm170) cc_final: 0.8770 (ttp-170) REVERT: N 621 GLU cc_start: 0.9261 (pt0) cc_final: 0.8550 (pp20) REVERT: N 632 ASP cc_start: 0.9008 (t70) cc_final: 0.8447 (t0) REVERT: O 84 SER cc_start: 0.9385 (m) cc_final: 0.9111 (t) REVERT: P 5 THR cc_start: 0.7893 (m) cc_final: 0.7492 (p) REVERT: P 55 GLU cc_start: 0.8453 (tp30) cc_final: 0.8165 (tp30) REVERT: P 58 VAL cc_start: 0.8445 (t) cc_final: 0.8033 (p) REVERT: P 77 ASN cc_start: 0.8425 (t0) cc_final: 0.8145 (t0) REVERT: P 103 ARG cc_start: 0.8104 (ptt180) cc_final: 0.7851 (ttp-110) REVERT: Q 27 ASP cc_start: 0.5516 (t0) cc_final: 0.4954 (t0) REVERT: Q 32 TYR cc_start: 0.8606 (m-10) cc_final: 0.8175 (m-10) REVERT: Q 54 ARG cc_start: 0.8354 (ptp90) cc_final: 0.8128 (mmp80) REVERT: Q 86 ASP cc_start: 0.8624 (t0) cc_final: 0.8348 (t0) REVERT: R 20 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.7569 (mpp80) REVERT: R 70 ARG cc_start: 0.7566 (mmm160) cc_final: 0.7209 (mmp-170) REVERT: R 79 GLU cc_start: 0.8501 (tp30) cc_final: 0.7994 (tp30) outliers start: 69 outliers final: 59 residues processed: 316 average time/residue: 0.4162 time to fit residues: 198.7611 Evaluate side-chains 315 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 251 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 425 ASN Chi-restraints excluded: chain M residue 488 VAL Chi-restraints excluded: chain N residue 638 TYR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 86 optimal weight: 0.9980 chunk 270 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 258 optimal weight: 0.0970 chunk 2 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 140 optimal weight: 0.3980 chunk 227 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 287 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN M 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.082991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.057005 restraints weight = 63034.605| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.60 r_work: 0.2762 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26835 Z= 0.102 Angle : 0.580 10.404 36699 Z= 0.276 Chirality : 0.043 0.278 4374 Planarity : 0.003 0.052 4440 Dihedral : 7.522 80.983 6087 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.06 % Allowed : 16.69 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.16), residues: 3021 helix: 0.27 (0.29), residues: 381 sheet: -0.11 (0.18), residues: 942 loop : -1.32 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 69 HIS 0.003 0.001 HIS G 374 PHE 0.008 0.001 PHE A 159 TYR 0.009 0.001 TYR D 91 ARG 0.013 0.001 ARG M 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 63) link_NAG-ASN : angle 1.62374 ( 189) link_ALPHA1-6 : bond 0.00742 ( 15) link_ALPHA1-6 : angle 1.42359 ( 45) link_BETA1-4 : bond 0.00506 ( 36) link_BETA1-4 : angle 1.45561 ( 108) link_ALPHA1-2 : bond 0.00601 ( 9) link_ALPHA1-2 : angle 1.49571 ( 27) link_ALPHA1-3 : bond 0.01067 ( 12) link_ALPHA1-3 : angle 1.42228 ( 36) hydrogen bonds : bond 0.02660 ( 480) hydrogen bonds : angle 4.67481 ( 1224) SS BOND : bond 0.00352 ( 45) SS BOND : angle 0.77851 ( 90) covalent geometry : bond 0.00237 (26655) covalent geometry : angle 0.55967 (36204) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 267 time to evaluate : 2.854 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: G 69 TRP cc_start: 0.6922 (m-90) cc_final: 0.6548 (m-90) REVERT: G 271 MET cc_start: 0.8535 (tpt) cc_final: 0.8194 (mmp) REVERT: B 592 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7896 (tp) REVERT: B 632 ASP cc_start: 0.9049 (t70) cc_final: 0.8552 (t0) REVERT: C 5 LEU cc_start: 0.8516 (tp) cc_final: 0.8165 (tp) REVERT: C 23 GLU cc_start: 0.7668 (mp0) cc_final: 0.7302 (mp0) REVERT: C 30 ARG cc_start: 0.8171 (mtt90) cc_final: 0.7699 (mtt180) REVERT: C 53 LYS cc_start: 0.9446 (ttmt) cc_final: 0.9101 (ttmm) REVERT: C 82 LYS cc_start: 0.7940 (tttp) cc_final: 0.7355 (tppt) REVERT: D 5 THR cc_start: 0.7893 (m) cc_final: 0.7544 (p) REVERT: D 58 VAL cc_start: 0.8447 (t) cc_final: 0.8074 (p) REVERT: D 60 SER cc_start: 0.8503 (t) cc_final: 0.8250 (m) REVERT: D 103 ARG cc_start: 0.8051 (ptt180) cc_final: 0.7757 (ttp-110) REVERT: H 86 ASP cc_start: 0.8402 (t0) cc_final: 0.8160 (t0) REVERT: H 100 MET cc_start: 0.8225 (mmt) cc_final: 0.7615 (mmt) REVERT: L 70 ARG cc_start: 0.7314 (mmm160) cc_final: 0.7091 (mmp-170) REVERT: L 79 GLU cc_start: 0.8405 (tp30) cc_final: 0.8032 (tp30) REVERT: L 87 TYR cc_start: 0.8274 (m-80) cc_final: 0.7713 (m-80) REVERT: A 475 MET cc_start: 0.8304 (mmm) cc_final: 0.7975 (mmt) REVERT: A 502 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8299 (tptp) REVERT: E 626 MET cc_start: 0.8328 (mtp) cc_final: 0.7851 (mtt) REVERT: E 632 ASP cc_start: 0.8972 (t70) cc_final: 0.8579 (t0) REVERT: E 634 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8483 (mt-10) REVERT: F 5 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8191 (mm) REVERT: F 23 GLU cc_start: 0.7772 (mp0) cc_final: 0.7417 (mp0) REVERT: F 82 LYS cc_start: 0.7962 (tttp) cc_final: 0.7637 (ttmm) REVERT: F 98 ASP cc_start: 0.8942 (m-30) cc_final: 0.7732 (t0) REVERT: F 100 ASP cc_start: 0.8202 (m-30) cc_final: 0.7868 (p0) REVERT: I 1 ASP cc_start: 0.8109 (p0) cc_final: 0.7840 (p0) REVERT: I 5 THR cc_start: 0.8095 (m) cc_final: 0.7487 (p) REVERT: I 24 GLN cc_start: 0.8174 (mt0) cc_final: 0.7693 (mp10) REVERT: I 58 VAL cc_start: 0.8467 (t) cc_final: 0.8116 (p) REVERT: I 103 ARG cc_start: 0.8100 (ptt180) cc_final: 0.7842 (ttp-110) REVERT: J 5 GLN cc_start: 0.9136 (tp-100) cc_final: 0.8934 (tp-100) REVERT: J 54 ARG cc_start: 0.8764 (mtt90) cc_final: 0.8158 (mmp80) REVERT: J 86 ASP cc_start: 0.8457 (t0) cc_final: 0.8162 (t0) REVERT: K 17 GLU cc_start: 0.6646 (pm20) cc_final: 0.6439 (pm20) REVERT: K 26 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7998 (tp-100) REVERT: K 79 GLU cc_start: 0.8414 (tp30) cc_final: 0.7862 (tp30) REVERT: K 90 MET cc_start: 0.9019 (tpp) cc_final: 0.8724 (tpp) REVERT: M 69 TRP cc_start: 0.6967 (m-90) cc_final: 0.6256 (m-90) REVERT: M 475 MET cc_start: 0.8540 (mmm) cc_final: 0.8331 (mmm) REVERT: M 504 ARG cc_start: 0.8404 (mmm160) cc_final: 0.8148 (mmm160) REVERT: N 542 ARG cc_start: 0.9118 (ttm170) cc_final: 0.8721 (ttp-170) REVERT: N 621 GLU cc_start: 0.9224 (pt0) cc_final: 0.8541 (pp20) REVERT: N 632 ASP cc_start: 0.8943 (t70) cc_final: 0.8382 (t0) REVERT: O 84 SER cc_start: 0.9357 (m) cc_final: 0.9041 (t) REVERT: O 100 ASP cc_start: 0.8344 (m-30) cc_final: 0.7925 (p0) REVERT: P 5 THR cc_start: 0.7760 (m) cc_final: 0.7405 (p) REVERT: P 55 GLU cc_start: 0.8341 (tp30) cc_final: 0.8088 (tp30) REVERT: P 58 VAL cc_start: 0.8414 (t) cc_final: 0.7976 (p) REVERT: P 77 ASN cc_start: 0.8474 (t0) cc_final: 0.8238 (t0) REVERT: P 103 ARG cc_start: 0.8145 (ptt180) cc_final: 0.7868 (ttp-110) REVERT: Q 27 ASP cc_start: 0.5879 (t0) cc_final: 0.5358 (t0) REVERT: Q 32 TYR cc_start: 0.8600 (m-10) cc_final: 0.8163 (m-10) REVERT: Q 54 ARG cc_start: 0.8333 (ptp90) cc_final: 0.8103 (mmp80) REVERT: Q 86 ASP cc_start: 0.8658 (t0) cc_final: 0.8366 (t0) REVERT: R 20 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7541 (mpp80) REVERT: R 26 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7907 (mm-40) REVERT: R 79 GLU cc_start: 0.8501 (tp30) cc_final: 0.7988 (tp30) outliers start: 55 outliers final: 47 residues processed: 318 average time/residue: 0.4331 time to fit residues: 209.5601 Evaluate side-chains 309 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 258 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 425 ASN Chi-restraints excluded: chain M residue 488 VAL Chi-restraints excluded: chain N residue 638 TYR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 66 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 200 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 203 optimal weight: 9.9990 chunk 120 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 265 optimal weight: 5.9990 chunk 294 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 465 ASN ** M 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.082962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.056980 restraints weight = 63354.274| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.61 r_work: 0.2760 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 26835 Z= 0.127 Angle : 0.696 59.200 36699 Z= 0.365 Chirality : 0.043 0.273 4374 Planarity : 0.004 0.056 4440 Dihedral : 7.531 81.012 6087 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.21 % Allowed : 16.76 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.07 (0.16), residues: 3021 helix: 0.27 (0.29), residues: 381 sheet: -0.09 (0.18), residues: 942 loop : -1.32 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 69 HIS 0.002 0.000 HIS G 374 PHE 0.007 0.001 PHE A 159 TYR 0.010 0.001 TYR D 91 ARG 0.015 0.000 ARG I 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 63) link_NAG-ASN : angle 1.62444 ( 189) link_ALPHA1-6 : bond 0.00755 ( 15) link_ALPHA1-6 : angle 1.43626 ( 45) link_BETA1-4 : bond 0.00528 ( 36) link_BETA1-4 : angle 1.45747 ( 108) link_ALPHA1-2 : bond 0.00623 ( 9) link_ALPHA1-2 : angle 1.48786 ( 27) link_ALPHA1-3 : bond 0.01071 ( 12) link_ALPHA1-3 : angle 1.40773 ( 36) hydrogen bonds : bond 0.02696 ( 480) hydrogen bonds : angle 4.67934 ( 1224) SS BOND : bond 0.00376 ( 45) SS BOND : angle 0.77687 ( 90) covalent geometry : bond 0.00290 (26655) covalent geometry : angle 0.68047 (36204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11377.02 seconds wall clock time: 198 minutes 30.46 seconds (11910.46 seconds total)