Starting phenix.real_space_refine on Sun Jun 22 14:35:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bew_44484/06_2025/9bew_44484.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bew_44484/06_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_44484/06_2025/9bew_44484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bew_44484/06_2025/9bew_44484.map" model { file = "/net/cci-nas-00/data/ceres_data/9bew_44484/06_2025/9bew_44484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bew_44484/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 17.32, per 1000 atoms: 0.66 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: 7.37 Conformation dependent library (CDL) restraints added in 2.9 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: 3.11 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: 8.57 Time building geometry restraints manager: 8.56 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: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.030 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 59.310 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.980 ------------------------------------------------------------------------------- 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 : 2.800 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: 0.5297 time to fit residues: 349.0759 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 : 2.970 ------------------------------------------------------------------------------- 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 = 38)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.059858 restraints weight = 63117.663| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.51 r_work: 0.2829 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 1.81029 ( 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 : 3.430 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: 0.7963 (mtt90) REVERT: C 53 LYS cc_start: 0.9503 (ttmt) cc_final: 0.9197 (ttmm) REVERT: C 82 LYS cc_start: 0.8089 (tttp) cc_final: 0.7878 (ttmm) REVERT: C 98 ASP cc_start: 0.9033 (m-30) cc_final: 0.8223 (t0) REVERT: D 77 ASN cc_start: 0.8245 (t0) cc_final: 0.7841 (t0) REVERT: H 86 ASP cc_start: 0.8506 (t0) cc_final: 0.8228 (t0) REVERT: H 90 TYR cc_start: 0.7907 (m-10) cc_final: 0.7576 (m-10) REVERT: L 66 ASP cc_start: 0.7876 (t0) cc_final: 0.7108 (t0) REVERT: L 79 GLU cc_start: 0.8544 (tp30) cc_final: 0.8182 (tp30) REVERT: E 584 GLU cc_start: 0.8651 (mt-10) cc_final: 0.7967 (mt-10) REVERT: E 632 ASP cc_start: 0.9016 (t70) cc_final: 0.8584 (t0) REVERT: F 53 LYS cc_start: 0.9497 (ttmt) cc_final: 0.9188 (ttmm) REVERT: F 82 LYS cc_start: 0.8095 (tttp) cc_final: 0.7839 (ttmm) REVERT: F 98 ASP cc_start: 0.8966 (m-30) cc_final: 0.8163 (t0) REVERT: I 24 GLN cc_start: 0.8405 (mt0) cc_final: 0.8176 (mp10) REVERT: I 58 VAL cc_start: 0.8762 (t) cc_final: 0.8441 (p) REVERT: I 77 ASN cc_start: 0.7962 (t0) cc_final: 0.7694 (t0) REVERT: J 54 ARG cc_start: 0.8472 (mtt90) cc_final: 0.7934 (mmp80) REVERT: K 79 GLU cc_start: 0.8673 (tp30) cc_final: 0.8082 (tp30) REVERT: M 69 TRP cc_start: 0.7297 (m-90) cc_final: 0.6660 (m-90) REVERT: M 475 MET cc_start: 0.8295 (tpp) cc_final: 0.7915 (mmm) REVERT: N 530 MET cc_start: 0.8775 (mtp) cc_final: 0.8452 (mtp) REVERT: N 542 ARG cc_start: 0.9139 (ttm170) cc_final: 0.8869 (ttp-170) REVERT: N 632 ASP cc_start: 0.9047 (t70) cc_final: 0.8525 (t0) REVERT: O 84 SER cc_start: 0.9228 (m) cc_final: 0.8969 (t) REVERT: O 98 ASP cc_start: 0.9035 (m-30) cc_final: 0.8281 (t0) REVERT: P 55 GLU cc_start: 0.7565 (tp30) cc_final: 0.7110 (tp30) REVERT: P 77 ASN cc_start: 0.7817 (t0) cc_final: 0.7363 (t0) REVERT: Q 46 GLU cc_start: 0.8472 (tt0) cc_final: 0.8116 (tt0) REVERT: Q 86 ASP cc_start: 0.8448 (t0) cc_final: 0.8208 (t0) REVERT: Q 90 TYR cc_start: 0.7798 (m-10) cc_final: 0.7485 (m-10) REVERT: R 42 GLN cc_start: 0.8752 (tp40) cc_final: 0.7966 (mp10) REVERT: R 79 GLU cc_start: 0.8685 (tp30) cc_final: 0.8127 (tp30) outliers start: 31 outliers final: 20 residues processed: 316 average time/residue: 0.4462 time to fit residues: 212.1499 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 : 2.990 ------------------------------------------------------------------------------- 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: 0.9990 chunk 138 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 283 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.083926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.057710 restraints weight = 63090.740| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.64 r_work: 0.2772 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26835 Z= 0.171 Angle : 0.590 9.793 36699 Z= 0.281 Chirality : 0.045 0.295 4374 Planarity : 0.004 0.052 4440 Dihedral : 9.530 85.111 6087 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.39 % Allowed : 12.49 % Favored : 86.13 % 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: -2.35 (0.14), residues: 3021 helix: -1.57 (0.25), residues: 381 sheet: -1.15 (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 A 85 PHE 0.010 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 0.00234 ( 63) link_NAG-ASN : angle 1.74629 ( 189) link_ALPHA1-6 : bond 0.00753 ( 15) link_ALPHA1-6 : angle 1.61615 ( 45) link_BETA1-4 : bond 0.00558 ( 36) link_BETA1-4 : angle 1.89203 ( 108) link_ALPHA1-2 : bond 0.00617 ( 9) link_ALPHA1-2 : angle 1.90604 ( 27) link_ALPHA1-3 : bond 0.01094 ( 12) link_ALPHA1-3 : angle 1.80148 ( 36) hydrogen bonds : bond 0.03890 ( 480) hydrogen bonds : angle 5.58963 ( 1224) SS BOND : bond 0.00333 ( 45) SS BOND : angle 1.11540 ( 90) covalent geometry : bond 0.00397 (26655) covalent geometry : angle 0.56025 (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 324 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 287 time to evaluate : 3.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 69 TRP cc_start: 0.6899 (m-90) cc_final: 0.6143 (m-90) REVERT: G 271 MET cc_start: 0.8493 (tpt) cc_final: 0.8247 (mmp) REVERT: B 632 ASP cc_start: 0.9077 (t70) cc_final: 0.8582 (t0) REVERT: C 30 ARG cc_start: 0.8197 (mtt90) cc_final: 0.7915 (mtt90) REVERT: C 53 LYS cc_start: 0.9435 (ttmt) cc_final: 0.9108 (ttmm) REVERT: C 82 LYS cc_start: 0.7963 (tttp) cc_final: 0.7687 (ttmm) REVERT: C 98 ASP cc_start: 0.9010 (m-30) cc_final: 0.8105 (t0) REVERT: D 55 GLU cc_start: 0.7996 (tp30) cc_final: 0.7786 (tp30) REVERT: D 77 ASN cc_start: 0.8367 (t0) cc_final: 0.7970 (t0) REVERT: H 54 ARG cc_start: 0.8559 (mtt90) cc_final: 0.8035 (mmp80) REVERT: H 86 ASP cc_start: 0.8547 (t0) cc_final: 0.8218 (t0) REVERT: H 90 TYR cc_start: 0.7831 (m-10) cc_final: 0.7528 (m-10) REVERT: L 66 ASP cc_start: 0.7902 (t0) cc_final: 0.7100 (t0) REVERT: L 79 GLU cc_start: 0.8468 (tp30) cc_final: 0.8122 (tp30) REVERT: E 584 GLU cc_start: 0.8553 (mt-10) cc_final: 0.7970 (mt-10) REVERT: E 632 ASP cc_start: 0.9005 (t70) cc_final: 0.8566 (t0) REVERT: E 634 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8337 (mt-10) REVERT: F 23 GLU cc_start: 0.7673 (mp0) cc_final: 0.7383 (mp0) REVERT: F 53 LYS cc_start: 0.9421 (ttmt) cc_final: 0.9049 (ttmm) REVERT: F 82 LYS cc_start: 0.7896 (tttp) cc_final: 0.7599 (ttmm) REVERT: F 84 SER cc_start: 0.9301 (m) cc_final: 0.9077 (t) REVERT: F 98 ASP cc_start: 0.8942 (m-30) cc_final: 0.8002 (t0) REVERT: I 24 GLN cc_start: 0.8254 (mt0) cc_final: 0.7972 (mp10) REVERT: I 58 VAL cc_start: 0.8639 (t) cc_final: 0.8307 (p) REVERT: I 77 ASN cc_start: 0.8208 (t0) cc_final: 0.7790 (t0) REVERT: I 103 ARG cc_start: 0.8047 (ptt180) cc_final: 0.7783 (ttp-110) REVERT: J 54 ARG cc_start: 0.8565 (mtt90) cc_final: 0.8040 (mmp80) REVERT: K 66 ASP cc_start: 0.7776 (t0) cc_final: 0.7319 (t0) REVERT: K 79 GLU cc_start: 0.8582 (tp30) cc_final: 0.8003 (tp30) REVERT: M 69 TRP cc_start: 0.7241 (m-90) cc_final: 0.6522 (m-90) REVERT: N 542 ARG cc_start: 0.9173 (ttm170) cc_final: 0.8811 (ttp-170) REVERT: N 632 ASP cc_start: 0.9035 (t70) cc_final: 0.8509 (t0) REVERT: O 30 ARG cc_start: 0.8329 (mtt90) cc_final: 0.7847 (mtt180) REVERT: O 80 MET cc_start: 0.8973 (tmm) cc_final: 0.8557 (tmm) REVERT: O 84 SER cc_start: 0.9300 (m) cc_final: 0.9039 (t) REVERT: O 98 ASP cc_start: 0.8953 (m-30) cc_final: 0.8050 (t0) REVERT: P 55 GLU cc_start: 0.7962 (tp30) cc_final: 0.7502 (tp30) REVERT: P 77 ASN cc_start: 0.7972 (t0) cc_final: 0.7590 (t0) REVERT: P 103 ARG cc_start: 0.8188 (ptt180) cc_final: 0.7898 (ttp-110) REVERT: Q 27 ASP cc_start: 0.7617 (t0) cc_final: 0.7363 (t0) REVERT: Q 32 TYR cc_start: 0.8479 (m-10) cc_final: 0.8177 (m-10) REVERT: Q 46 GLU cc_start: 0.8473 (tt0) cc_final: 0.8259 (tt0) REVERT: Q 86 ASP cc_start: 0.8432 (t0) cc_final: 0.8164 (t0) REVERT: Q 90 TYR cc_start: 0.7695 (m-10) cc_final: 0.7411 (m-10) REVERT: Q 97 ARG cc_start: 0.9017 (tmm-80) cc_final: 0.8297 (ttp80) REVERT: R 70 ARG cc_start: 0.7252 (mmm160) cc_final: 0.6766 (mmp-170) REVERT: R 79 GLU cc_start: 0.8591 (tp30) cc_final: 0.8042 (tp30) outliers start: 37 outliers final: 33 residues processed: 318 average time/residue: 0.4303 time to fit residues: 206.7961 Evaluate side-chains 308 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 275 time to evaluate : 3.060 ------------------------------------------------------------------------------- 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 Q residue 68 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: 0.8980 chunk 179 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 290 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 84 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.082822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.056598 restraints weight = 63799.636| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.65 r_work: 0.2746 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26835 Z= 0.179 Angle : 0.596 10.061 36699 Z= 0.284 Chirality : 0.045 0.306 4374 Planarity : 0.004 0.044 4440 Dihedral : 8.416 85.081 6087 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.06 % Allowed : 13.46 % Favored : 84.48 % 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: -1.82 (0.15), residues: 3021 helix: -0.76 (0.28), residues: 366 sheet: -0.73 (0.17), residues: 918 loop : -1.59 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 69 HIS 0.002 0.001 HIS M 85 PHE 0.011 0.001 PHE I 87 TYR 0.009 0.001 TYR K 87 ARG 0.009 0.001 ARG M 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 63) link_NAG-ASN : angle 1.79313 ( 189) link_ALPHA1-6 : bond 0.00838 ( 15) link_ALPHA1-6 : angle 1.49810 ( 45) link_BETA1-4 : bond 0.00462 ( 36) link_BETA1-4 : angle 1.77805 ( 108) link_ALPHA1-2 : bond 0.00537 ( 9) link_ALPHA1-2 : angle 1.61586 ( 27) link_ALPHA1-3 : bond 0.01071 ( 12) link_ALPHA1-3 : angle 1.61408 ( 36) hydrogen bonds : bond 0.03425 ( 480) hydrogen bonds : angle 5.26163 ( 1224) SS BOND : bond 0.00332 ( 45) SS BOND : angle 0.96321 ( 90) covalent geometry : bond 0.00419 (26655) covalent geometry : angle 0.56926 (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 340 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 285 time to evaluate : 2.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 69 TRP cc_start: 0.6987 (m-90) cc_final: 0.6428 (m-90) REVERT: G 205 CYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7944 (m) REVERT: G 271 MET cc_start: 0.8505 (tpt) cc_final: 0.8263 (mmp) REVERT: B 632 ASP cc_start: 0.9054 (t70) cc_final: 0.8630 (t0) REVERT: B 634 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8280 (mp0) REVERT: C 30 ARG cc_start: 0.8209 (mtt90) cc_final: 0.7837 (mtt180) REVERT: C 53 LYS cc_start: 0.9436 (ttmt) cc_final: 0.9113 (ttmm) REVERT: C 82 LYS cc_start: 0.7940 (tttp) cc_final: 0.7692 (ttmm) REVERT: C 98 ASP cc_start: 0.8945 (m-30) cc_final: 0.7953 (t0) REVERT: D 55 GLU cc_start: 0.8235 (tp30) cc_final: 0.7985 (tp30) REVERT: D 77 ASN cc_start: 0.8419 (t0) cc_final: 0.7929 (t0) REVERT: D 103 ARG cc_start: 0.8078 (ptt180) cc_final: 0.7819 (ttp-110) REVERT: H 54 ARG cc_start: 0.8544 (mtt90) cc_final: 0.8108 (mmp80) REVERT: H 86 ASP cc_start: 0.8457 (t0) cc_final: 0.8080 (t0) REVERT: H 90 TYR cc_start: 0.7708 (m-10) cc_final: 0.7427 (m-10) REVERT: L 26 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8067 (mm-40) REVERT: L 66 ASP cc_start: 0.8089 (t0) cc_final: 0.7822 (t0) REVERT: L 79 GLU cc_start: 0.8439 (tp30) cc_final: 0.8091 (tp30) REVERT: A 161 MET cc_start: 0.8460 (tpt) cc_final: 0.8239 (mmm) REVERT: A 205 CYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7606 (m) REVERT: E 584 GLU cc_start: 0.8551 (mt-10) cc_final: 0.7945 (mt-10) REVERT: E 632 ASP cc_start: 0.8996 (t70) cc_final: 0.8577 (t0) REVERT: F 23 GLU cc_start: 0.7734 (mp0) cc_final: 0.7465 (mp0) REVERT: F 82 LYS cc_start: 0.7913 (tttp) cc_final: 0.7631 (ttmm) REVERT: F 84 SER cc_start: 0.9328 (m) cc_final: 0.9084 (t) REVERT: F 98 ASP cc_start: 0.8956 (m-30) cc_final: 0.7878 (t0) REVERT: F 100 ASP cc_start: 0.8401 (m-30) cc_final: 0.7845 (p0) REVERT: I 5 THR cc_start: 0.8107 (m) cc_final: 0.7553 (p) REVERT: I 24 GLN cc_start: 0.8197 (mt0) cc_final: 0.7827 (mp10) REVERT: I 55 GLU cc_start: 0.8417 (tp30) cc_final: 0.8179 (tp30) REVERT: I 58 VAL cc_start: 0.8574 (t) cc_final: 0.8250 (p) REVERT: I 77 ASN cc_start: 0.8475 (t0) cc_final: 0.8078 (t0) REVERT: I 103 ARG cc_start: 0.8060 (ptt180) cc_final: 0.7818 (ttp-110) REVERT: J 54 ARG cc_start: 0.8582 (mtt90) cc_final: 0.8081 (mmp80) REVERT: J 86 ASP cc_start: 0.8419 (t0) cc_final: 0.8170 (t0) REVERT: K 26 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8092 (mm-40) REVERT: K 70 ARG cc_start: 0.7148 (mmm160) cc_final: 0.6370 (mmp-170) REVERT: K 79 GLU cc_start: 0.8531 (tp30) cc_final: 0.7970 (tp30) REVERT: K 90 MET cc_start: 0.9016 (tpp) cc_final: 0.8761 (tpp) REVERT: M 69 TRP cc_start: 0.7239 (m-90) cc_final: 0.6488 (m-90) REVERT: M 205 CYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7824 (m) REVERT: M 475 MET cc_start: 0.8559 (mmm) cc_final: 0.8093 (mmm) REVERT: N 542 ARG cc_start: 0.9141 (ttm170) cc_final: 0.8772 (ttp-170) REVERT: N 621 GLU cc_start: 0.9239 (pt0) cc_final: 0.8594 (pp20) REVERT: N 632 ASP cc_start: 0.9031 (t70) cc_final: 0.8506 (t0) REVERT: O 84 SER cc_start: 0.9337 (m) cc_final: 0.9069 (t) REVERT: O 98 ASP cc_start: 0.8951 (m-30) cc_final: 0.7971 (t0) REVERT: P 55 GLU cc_start: 0.8233 (tp30) cc_final: 0.7839 (tp30) REVERT: P 77 ASN cc_start: 0.8088 (t0) cc_final: 0.7728 (t0) REVERT: P 103 ARG cc_start: 0.8146 (ptt180) cc_final: 0.7882 (ttp-110) REVERT: Q 27 ASP cc_start: 0.7627 (t0) cc_final: 0.7368 (t0) REVERT: Q 32 TYR cc_start: 0.8510 (m-10) cc_final: 0.8141 (m-10) REVERT: Q 54 ARG cc_start: 0.8291 (ptp90) cc_final: 0.7964 (mmp80) REVERT: Q 86 ASP cc_start: 0.8272 (t0) cc_final: 0.8061 (t0) REVERT: Q 90 TYR cc_start: 0.7771 (m-10) cc_final: 0.7548 (m-10) REVERT: R 20 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.7589 (mpp80) REVERT: R 70 ARG cc_start: 0.7327 (mmm160) cc_final: 0.6988 (mmp-170) REVERT: R 79 GLU cc_start: 0.8569 (tp30) cc_final: 0.8047 (tp30) outliers start: 55 outliers final: 40 residues processed: 332 average time/residue: 0.4265 time to fit residues: 214.7791 Evaluate side-chains 318 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 274 time to evaluate : 3.064 ------------------------------------------------------------------------------- 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 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 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 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 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 17 ASP Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 92 ASP 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 21 ILE Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain Q residue 24 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 109 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.083894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.057748 restraints weight = 62978.860| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.64 r_work: 0.2776 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26835 Z= 0.109 Angle : 0.551 9.847 36699 Z= 0.261 Chirality : 0.043 0.279 4374 Planarity : 0.003 0.037 4440 Dihedral : 8.005 82.736 6087 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.25 % Allowed : 14.14 % Favored : 83.61 % 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: -1.51 (0.15), residues: 3021 helix: -0.42 (0.28), residues: 366 sheet: -0.50 (0.17), residues: 912 loop : -1.42 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 69 HIS 0.001 0.000 HIS A 374 PHE 0.008 0.001 PHE M 53 TYR 0.008 0.001 TYR I 91 ARG 0.008 0.000 ARG D 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 63) link_NAG-ASN : angle 1.64853 ( 189) link_ALPHA1-6 : bond 0.00822 ( 15) link_ALPHA1-6 : angle 1.53295 ( 45) link_BETA1-4 : bond 0.00491 ( 36) link_BETA1-4 : angle 1.57159 ( 108) link_ALPHA1-2 : bond 0.00575 ( 9) link_ALPHA1-2 : angle 1.53954 ( 27) link_ALPHA1-3 : bond 0.01063 ( 12) link_ALPHA1-3 : angle 1.50379 ( 36) hydrogen bonds : bond 0.02971 ( 480) hydrogen bonds : angle 5.04354 ( 1224) SS BOND : bond 0.00417 ( 45) SS BOND : angle 0.79571 ( 90) covalent geometry : bond 0.00249 (26655) covalent geometry : angle 0.52647 (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 348 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 288 time to evaluate : 3.032 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: 0.7045 (m-90) cc_final: 0.6471 (m-90) REVERT: G 271 MET cc_start: 0.8474 (tpt) cc_final: 0.8214 (mmp) REVERT: G 475 MET cc_start: 0.8216 (mmm) cc_final: 0.7943 (mmm) REVERT: B 632 ASP cc_start: 0.9040 (t70) cc_final: 0.8593 (t0) REVERT: B 634 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8316 (mp0) REVERT: C 30 ARG cc_start: 0.8185 (mtt90) cc_final: 0.7741 (mtt180) REVERT: C 53 LYS cc_start: 0.9438 (ttmt) cc_final: 0.9123 (ttmm) REVERT: C 82 LYS cc_start: 0.7956 (tttp) cc_final: 0.7695 (ttmm) REVERT: C 98 ASP cc_start: 0.8938 (m-30) cc_final: 0.7923 (t0) REVERT: D 5 THR cc_start: 0.7799 (m) cc_final: 0.7472 (p) REVERT: D 55 GLU cc_start: 0.8249 (tp30) cc_final: 0.7990 (tp30) REVERT: D 77 ASN cc_start: 0.8427 (t0) cc_final: 0.7950 (t0) REVERT: D 103 ARG cc_start: 0.8050 (ptt180) cc_final: 0.7792 (ttp-110) REVERT: H 54 ARG cc_start: 0.8549 (mtt90) cc_final: 0.8066 (mmp80) REVERT: H 86 ASP cc_start: 0.8496 (t0) cc_final: 0.8103 (t0) REVERT: H 90 TYR cc_start: 0.7666 (m-10) cc_final: 0.7412 (m-10) REVERT: L 26 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8094 (mm-40) REVERT: L 66 ASP cc_start: 0.8050 (t0) cc_final: 0.7785 (t0) REVERT: L 79 GLU cc_start: 0.8437 (tp30) cc_final: 0.8081 (tp30) REVERT: A 69 TRP cc_start: 0.6695 (m-90) cc_final: 0.6434 (m-90) REVERT: A 161 MET cc_start: 0.8395 (tpt) cc_final: 0.8163 (mmm) REVERT: E 584 GLU cc_start: 0.8534 (mt-10) cc_final: 0.7890 (mt-10) REVERT: E 632 ASP cc_start: 0.8956 (t70) cc_final: 0.8525 (t0) REVERT: F 23 GLU cc_start: 0.7721 (mp0) cc_final: 0.7425 (mp0) REVERT: F 82 LYS cc_start: 0.7891 (tttp) cc_final: 0.7530 (ttmm) REVERT: F 98 ASP cc_start: 0.8920 (m-30) cc_final: 0.7817 (t0) REVERT: F 100 ASP cc_start: 0.8342 (m-30) cc_final: 0.7851 (p0) REVERT: I 5 THR cc_start: 0.8075 (m) cc_final: 0.7518 (p) REVERT: I 24 GLN cc_start: 0.8161 (mt0) cc_final: 0.7769 (mp10) REVERT: I 55 GLU cc_start: 0.8423 (tp30) cc_final: 0.8161 (tp30) REVERT: I 58 VAL cc_start: 0.8503 (t) cc_final: 0.8149 (p) REVERT: I 77 ASN cc_start: 0.8475 (t0) cc_final: 0.8190 (t0) REVERT: I 103 ARG cc_start: 0.8089 (ptt180) cc_final: 0.7845 (ttp-110) REVERT: J 86 ASP cc_start: 0.8397 (t0) cc_final: 0.8128 (t0) REVERT: K 26 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8098 (mm-40) REVERT: K 66 ASP cc_start: 0.7974 (t0) cc_final: 0.7476 (t0) REVERT: K 70 ARG cc_start: 0.7004 (mmm160) cc_final: 0.6237 (mmp-170) REVERT: K 79 GLU cc_start: 0.8537 (tp30) cc_final: 0.7964 (tp30) REVERT: K 90 MET cc_start: 0.9014 (tpp) cc_final: 0.8729 (tpp) REVERT: M 69 TRP cc_start: 0.7139 (m-90) cc_final: 0.6489 (m-90) REVERT: M 205 CYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7746 (m) REVERT: M 475 MET cc_start: 0.8487 (mmm) cc_final: 0.7992 (mmm) REVERT: M 504 ARG cc_start: 0.8430 (mmm160) cc_final: 0.8213 (mmm160) REVERT: N 542 ARG cc_start: 0.9110 (ttm170) cc_final: 0.8705 (ttp-170) REVERT: N 621 GLU cc_start: 0.9239 (pt0) cc_final: 0.8510 (pp20) REVERT: N 632 ASP cc_start: 0.8956 (t70) cc_final: 0.8415 (t0) REVERT: O 30 ARG cc_start: 0.8272 (mtt90) cc_final: 0.8010 (mtt90) REVERT: O 84 SER cc_start: 0.9332 (m) cc_final: 0.9055 (t) REVERT: O 98 ASP cc_start: 0.8919 (m-30) cc_final: 0.7923 (t0) REVERT: P 5 THR cc_start: 0.7850 (m) cc_final: 0.7529 (p) REVERT: P 55 GLU cc_start: 0.8185 (tp30) cc_final: 0.7814 (tp30) REVERT: P 58 VAL cc_start: 0.8456 (t) cc_final: 0.8043 (p) REVERT: P 77 ASN cc_start: 0.8352 (t0) cc_final: 0.8067 (t0) REVERT: P 103 ARG cc_start: 0.8141 (ptt180) cc_final: 0.7869 (ttp-110) REVERT: Q 27 ASP cc_start: 0.7752 (t0) cc_final: 0.7510 (t0) REVERT: Q 32 TYR cc_start: 0.8483 (m-10) cc_final: 0.8100 (m-10) REVERT: Q 86 ASP cc_start: 0.8291 (t0) cc_final: 0.8071 (t0) REVERT: Q 90 TYR cc_start: 0.7758 (m-10) cc_final: 0.7554 (m-10) REVERT: R 20 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7572 (mpp80) REVERT: R 70 ARG cc_start: 0.7275 (mmm160) cc_final: 0.6927 (mmp-170) REVERT: R 79 GLU cc_start: 0.8560 (tp30) cc_final: 0.8035 (tp30) outliers start: 60 outliers final: 42 residues processed: 340 average time/residue: 0.4284 time to fit residues: 220.7757 Evaluate side-chains 316 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 3.348 ------------------------------------------------------------------------------- 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 499 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 48 VAL 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 D residue 60 SER Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 33 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 488 VAL Chi-restraints excluded: chain A residue 499 THR 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 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 M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS 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 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: 0.9990 chunk 119 optimal weight: 6.9990 chunk 267 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 145 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 146 optimal weight: 0.0870 chunk 217 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.084353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.058266 restraints weight = 62841.832| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.63 r_work: 0.2787 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26835 Z= 0.100 Angle : 0.535 9.812 36699 Z= 0.254 Chirality : 0.043 0.273 4374 Planarity : 0.003 0.036 4440 Dihedral : 7.588 81.295 6087 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.17 % Allowed : 14.92 % Favored : 82.90 % 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: -1.32 (0.15), residues: 3021 helix: -0.25 (0.28), residues: 381 sheet: -0.23 (0.18), residues: 900 loop : -1.39 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 69 HIS 0.001 0.000 HIS G 374 PHE 0.011 0.001 PHE F 73 TYR 0.007 0.001 TYR G 484 ARG 0.007 0.000 ARG I 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 63) link_NAG-ASN : angle 1.56476 ( 189) link_ALPHA1-6 : bond 0.00824 ( 15) link_ALPHA1-6 : angle 1.48721 ( 45) link_BETA1-4 : bond 0.00486 ( 36) link_BETA1-4 : angle 1.52614 ( 108) link_ALPHA1-2 : bond 0.00599 ( 9) link_ALPHA1-2 : angle 1.48080 ( 27) link_ALPHA1-3 : bond 0.01059 ( 12) link_ALPHA1-3 : angle 1.40866 ( 36) hydrogen bonds : bond 0.02621 ( 480) hydrogen bonds : angle 4.82615 ( 1224) SS BOND : bond 0.00299 ( 45) SS BOND : angle 0.74538 ( 90) covalent geometry : bond 0.00231 (26655) covalent geometry : angle 0.51291 (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 340 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 282 time to evaluate : 2.997 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: 0.6998 (m-90) cc_final: 0.6446 (m-90) REVERT: G 271 MET cc_start: 0.8486 (tpt) cc_final: 0.8174 (mmp) REVERT: G 475 MET cc_start: 0.8231 (mmm) cc_final: 0.7919 (mmm) REVERT: B 632 ASP cc_start: 0.9024 (t70) cc_final: 0.8544 (t0) REVERT: C 30 ARG cc_start: 0.8176 (mtt90) cc_final: 0.7737 (mtt180) REVERT: C 53 LYS cc_start: 0.9443 (ttmt) cc_final: 0.9133 (ttmm) REVERT: C 82 LYS cc_start: 0.7981 (tttp) cc_final: 0.7726 (ttmm) REVERT: C 98 ASP cc_start: 0.8950 (m-30) cc_final: 0.7970 (t0) REVERT: D 5 THR cc_start: 0.7670 (m) cc_final: 0.7369 (p) REVERT: D 55 GLU cc_start: 0.8356 (tp30) cc_final: 0.8070 (tp30) REVERT: D 77 ASN cc_start: 0.8509 (t0) cc_final: 0.8116 (t0) REVERT: D 103 ARG cc_start: 0.8000 (ptt180) cc_final: 0.7724 (ttp-110) REVERT: H 54 ARG cc_start: 0.8519 (mtt90) cc_final: 0.8054 (mmp80) REVERT: H 86 ASP cc_start: 0.8452 (t0) cc_final: 0.8086 (t0) REVERT: H 90 TYR cc_start: 0.7673 (m-10) cc_final: 0.7444 (m-10) REVERT: L 26 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8117 (mm-40) REVERT: L 66 ASP cc_start: 0.8065 (t0) cc_final: 0.7860 (t0) REVERT: L 79 GLU cc_start: 0.8450 (tp30) cc_final: 0.8086 (tp30) REVERT: A 69 TRP cc_start: 0.6820 (m-90) cc_final: 0.6505 (m-90) REVERT: E 584 GLU cc_start: 0.8505 (mt-10) cc_final: 0.7991 (mt-10) REVERT: E 632 ASP cc_start: 0.8910 (t70) cc_final: 0.8464 (t0) REVERT: F 23 GLU cc_start: 0.7726 (mp0) cc_final: 0.7417 (mp0) REVERT: F 82 LYS cc_start: 0.7896 (tttp) cc_final: 0.7545 (ttmm) REVERT: F 98 ASP cc_start: 0.8942 (m-30) cc_final: 0.7831 (t0) REVERT: F 100 ASP cc_start: 0.8333 (m-30) cc_final: 0.7826 (p0) REVERT: I 5 THR cc_start: 0.8031 (m) cc_final: 0.7451 (p) REVERT: I 24 GLN cc_start: 0.8144 (mt0) cc_final: 0.7759 (mp10) REVERT: I 55 GLU cc_start: 0.8448 (tp30) cc_final: 0.8197 (tp30) REVERT: I 58 VAL cc_start: 0.8452 (t) cc_final: 0.8088 (p) REVERT: I 77 ASN cc_start: 0.8469 (t0) cc_final: 0.8209 (t0) REVERT: I 103 ARG cc_start: 0.8089 (ptt180) cc_final: 0.7842 (ttp-110) REVERT: J 86 ASP cc_start: 0.8397 (t0) cc_final: 0.8128 (t0) REVERT: K 26 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8026 (mm-40) REVERT: K 66 ASP cc_start: 0.8047 (t0) cc_final: 0.7527 (t0) REVERT: K 70 ARG cc_start: 0.7003 (mmm160) cc_final: 0.6227 (mmp-170) REVERT: K 79 GLU cc_start: 0.8545 (tp30) cc_final: 0.7966 (tp30) REVERT: K 90 MET cc_start: 0.9018 (tpp) cc_final: 0.8763 (tpp) REVERT: M 69 TRP cc_start: 0.7158 (m-90) cc_final: 0.6533 (m-90) REVERT: M 475 MET cc_start: 0.8533 (mmm) cc_final: 0.8095 (mmm) REVERT: N 542 ARG cc_start: 0.9035 (ttm170) cc_final: 0.8684 (ttp-170) REVERT: N 621 GLU cc_start: 0.9233 (pt0) cc_final: 0.8507 (pp20) REVERT: N 632 ASP cc_start: 0.8942 (t70) cc_final: 0.8403 (t0) REVERT: O 30 ARG cc_start: 0.8262 (mtt90) cc_final: 0.8002 (mtt90) REVERT: O 98 ASP cc_start: 0.8928 (m-30) cc_final: 0.7925 (t0) REVERT: P 5 THR cc_start: 0.7805 (m) cc_final: 0.7419 (p) REVERT: P 55 GLU cc_start: 0.8275 (tp30) cc_final: 0.7922 (tp30) REVERT: P 58 VAL cc_start: 0.8460 (t) cc_final: 0.8024 (p) REVERT: P 77 ASN cc_start: 0.8336 (t0) cc_final: 0.7966 (t0) REVERT: P 103 ARG cc_start: 0.8135 (ptt180) cc_final: 0.7864 (ttp-110) REVERT: Q 32 TYR cc_start: 0.8473 (m-10) cc_final: 0.8028 (m-10) REVERT: R 20 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7542 (mpp80) REVERT: R 70 ARG cc_start: 0.7317 (mmm160) cc_final: 0.6986 (mmp-170) REVERT: R 79 GLU cc_start: 0.8553 (tp30) cc_final: 0.8041 (tp30) outliers start: 58 outliers final: 46 residues processed: 331 average time/residue: 0.4498 time to fit residues: 226.8901 Evaluate side-chains 314 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 267 time to evaluate : 2.847 ------------------------------------------------------------------------------- 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 499 THR 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 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 60 SER 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 488 VAL Chi-restraints excluded: chain A residue 499 THR 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 I residue 90 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 68 VAL 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 M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 168 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 190 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 244 optimal weight: 5.9990 chunk 61 optimal weight: 0.3980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3467 r_free = 0.3467 target = 0.083881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.058571 restraints weight = 62918.850| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.30 r_work: 0.2808 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26835 Z= 0.154 Angle : 0.573 9.985 36699 Z= 0.273 Chirality : 0.044 0.298 4374 Planarity : 0.003 0.050 4440 Dihedral : 7.601 81.550 6087 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.25 % Allowed : 15.26 % Favored : 82.49 % 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: -1.20 (0.15), residues: 3021 helix: 0.05 (0.29), residues: 369 sheet: -0.25 (0.17), residues: 933 loop : -1.31 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 69 HIS 0.002 0.001 HIS G 72 PHE 0.011 0.001 PHE M 53 TYR 0.008 0.001 TYR P 91 ARG 0.010 0.000 ARG M 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 63) link_NAG-ASN : angle 1.65482 ( 189) link_ALPHA1-6 : bond 0.00765 ( 15) link_ALPHA1-6 : angle 1.47526 ( 45) link_BETA1-4 : bond 0.00455 ( 36) link_BETA1-4 : angle 1.58171 ( 108) link_ALPHA1-2 : bond 0.00512 ( 9) link_ALPHA1-2 : angle 1.59263 ( 27) link_ALPHA1-3 : bond 0.00995 ( 12) link_ALPHA1-3 : angle 1.43575 ( 36) hydrogen bonds : bond 0.02947 ( 480) hydrogen bonds : angle 4.76806 ( 1224) SS BOND : bond 0.00396 ( 45) SS BOND : angle 0.93755 ( 90) covalent geometry : bond 0.00361 (26655) covalent geometry : angle 0.55015 (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 332 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 272 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 69 TRP cc_start: 0.7215 (m-90) cc_final: 0.6819 (m-90) REVERT: G 205 CYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7865 (m) REVERT: G 271 MET cc_start: 0.8705 (tpt) cc_final: 0.8413 (mmp) REVERT: B 632 ASP cc_start: 0.9066 (t70) cc_final: 0.8580 (t0) REVERT: C 23 GLU cc_start: 0.7608 (mp0) cc_final: 0.7395 (mp0) REVERT: C 30 ARG cc_start: 0.8307 (mtt90) cc_final: 0.8065 (mtt90) REVERT: C 53 LYS cc_start: 0.9551 (ttmt) cc_final: 0.9259 (ttmm) REVERT: C 98 ASP cc_start: 0.8951 (m-30) cc_final: 0.8061 (t0) REVERT: D 5 THR cc_start: 0.7652 (m) cc_final: 0.7407 (p) REVERT: D 55 GLU cc_start: 0.8281 (tp30) cc_final: 0.7924 (tp30) REVERT: D 58 VAL cc_start: 0.8582 (t) cc_final: 0.8188 (p) REVERT: D 77 ASN cc_start: 0.8449 (t0) cc_final: 0.8104 (t0) REVERT: H 54 ARG cc_start: 0.8556 (mtt90) cc_final: 0.7988 (mmp80) REVERT: H 86 ASP cc_start: 0.8382 (t0) cc_final: 0.8105 (t0) REVERT: H 90 TYR cc_start: 0.7908 (m-10) cc_final: 0.7600 (m-10) REVERT: L 26 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8076 (mm-40) REVERT: L 66 ASP cc_start: 0.8370 (t0) cc_final: 0.8167 (t0) REVERT: L 79 GLU cc_start: 0.8571 (tp30) cc_final: 0.8139 (tp30) REVERT: A 69 TRP cc_start: 0.7233 (m-90) cc_final: 0.6970 (m-90) REVERT: E 632 ASP cc_start: 0.8847 (t70) cc_final: 0.8418 (t0) REVERT: F 23 GLU cc_start: 0.7897 (mp0) cc_final: 0.7648 (mp0) REVERT: F 82 LYS cc_start: 0.8190 (tttp) cc_final: 0.7865 (ttmm) REVERT: F 98 ASP cc_start: 0.8951 (m-30) cc_final: 0.8005 (t0) REVERT: F 100 ASP cc_start: 0.8307 (m-30) cc_final: 0.8062 (p0) REVERT: I 5 THR cc_start: 0.8044 (m) cc_final: 0.7552 (p) REVERT: I 24 GLN cc_start: 0.8298 (mt0) cc_final: 0.7917 (mp10) REVERT: I 55 GLU cc_start: 0.8355 (tp30) cc_final: 0.8119 (tp30) REVERT: I 58 VAL cc_start: 0.8633 (t) cc_final: 0.8282 (p) REVERT: I 77 ASN cc_start: 0.8466 (t0) cc_final: 0.8129 (t0) REVERT: J 86 ASP cc_start: 0.8398 (t0) cc_final: 0.8164 (t0) REVERT: K 70 ARG cc_start: 0.7395 (mmm160) cc_final: 0.6833 (mmp-170) REVERT: K 79 GLU cc_start: 0.8623 (tp30) cc_final: 0.8073 (tp30) REVERT: K 90 MET cc_start: 0.9128 (tpp) cc_final: 0.8874 (tpp) REVERT: M 69 TRP cc_start: 0.7292 (m-90) cc_final: 0.6768 (m-90) REVERT: M 205 CYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7757 (m) REVERT: N 542 ARG cc_start: 0.9146 (ttm170) cc_final: 0.8862 (ttp-170) REVERT: N 621 GLU cc_start: 0.9076 (pt0) cc_final: 0.8578 (pp20) REVERT: N 632 ASP cc_start: 0.8973 (t70) cc_final: 0.8430 (t0) REVERT: O 30 ARG cc_start: 0.8341 (mtt90) cc_final: 0.8120 (mtt90) REVERT: O 84 SER cc_start: 0.9333 (m) cc_final: 0.9044 (t) REVERT: O 98 ASP cc_start: 0.8960 (m-30) cc_final: 0.8109 (t0) REVERT: P 5 THR cc_start: 0.7798 (m) cc_final: 0.7470 (p) REVERT: P 55 GLU cc_start: 0.8256 (tp30) cc_final: 0.7934 (tp30) REVERT: P 58 VAL cc_start: 0.8588 (t) cc_final: 0.8171 (p) REVERT: P 77 ASN cc_start: 0.8188 (t0) cc_final: 0.7868 (t0) REVERT: Q 27 ASP cc_start: 0.6392 (t0) cc_final: 0.6021 (t0) REVERT: Q 32 TYR cc_start: 0.8625 (m-10) cc_final: 0.8317 (m-10) REVERT: Q 54 ARG cc_start: 0.8358 (ptp90) cc_final: 0.8015 (mmp80) REVERT: R 20 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.7572 (mpp80) REVERT: R 70 ARG cc_start: 0.7631 (mmm160) cc_final: 0.7329 (mmp-170) REVERT: R 79 GLU cc_start: 0.8665 (tp30) cc_final: 0.8134 (tp30) outliers start: 60 outliers final: 49 residues processed: 324 average time/residue: 0.4338 time to fit residues: 212.9413 Evaluate side-chains 316 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 264 time to evaluate : 2.952 ------------------------------------------------------------------------------- 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 499 THR 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 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 7 TYR 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 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 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 I residue 75 ILE Chi-restraints excluded: chain J residue 68 VAL 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 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 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: 0.4980 chunk 123 optimal weight: 0.0070 chunk 299 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 179 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 245 optimal weight: 0.9980 chunk 277 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.084639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.058949 restraints weight = 62942.893| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.42 r_work: 0.2812 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2918 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= 0.123 Angle : 0.566 10.973 36699 Z= 0.268 Chirality : 0.043 0.284 4374 Planarity : 0.003 0.050 4440 Dihedral : 7.472 80.683 6087 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.29 % Allowed : 15.64 % Favored : 82.08 % 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: -1.06 (0.15), residues: 3021 helix: 0.24 (0.29), residues: 369 sheet: -0.07 (0.18), residues: 906 loop : -1.29 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 69 HIS 0.001 0.000 HIS M 330 PHE 0.008 0.001 PHE G 53 TYR 0.008 0.001 TYR G 484 ARG 0.012 0.000 ARG M 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 63) link_NAG-ASN : angle 1.60719 ( 189) link_ALPHA1-6 : bond 0.00768 ( 15) link_ALPHA1-6 : angle 1.45927 ( 45) link_BETA1-4 : bond 0.00464 ( 36) link_BETA1-4 : angle 1.51618 ( 108) link_ALPHA1-2 : bond 0.00560 ( 9) link_ALPHA1-2 : angle 1.52130 ( 27) link_ALPHA1-3 : bond 0.01035 ( 12) link_ALPHA1-3 : angle 1.41909 ( 36) hydrogen bonds : bond 0.02749 ( 480) hydrogen bonds : angle 4.67196 ( 1224) SS BOND : bond 0.00384 ( 45) SS BOND : angle 0.83994 ( 90) covalent geometry : bond 0.00288 (26655) covalent geometry : angle 0.54420 (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 334 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 273 time to evaluate : 3.134 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: 0.7156 (m-90) cc_final: 0.6831 (m-90) REVERT: G 271 MET cc_start: 0.8719 (tpt) cc_final: 0.8423 (mmp) REVERT: B 632 ASP cc_start: 0.9038 (t70) cc_final: 0.8554 (t0) REVERT: C 30 ARG cc_start: 0.8310 (mtt90) cc_final: 0.7873 (mtt180) REVERT: C 53 LYS cc_start: 0.9537 (ttmt) cc_final: 0.9271 (ttmm) REVERT: C 98 ASP cc_start: 0.8954 (m-30) cc_final: 0.8077 (t0) REVERT: D 5 THR cc_start: 0.7588 (m) cc_final: 0.7302 (p) REVERT: D 55 GLU cc_start: 0.8253 (tp30) cc_final: 0.7910 (tp30) REVERT: D 58 VAL cc_start: 0.8555 (t) cc_final: 0.8146 (p) REVERT: D 60 SER cc_start: 0.8526 (t) cc_final: 0.8275 (m) REVERT: D 77 ASN cc_start: 0.8436 (t0) cc_final: 0.8189 (t0) REVERT: H 90 TYR cc_start: 0.7916 (m-10) cc_final: 0.7645 (m-10) REVERT: L 26 GLN cc_start: 0.8320 (mm-40) cc_final: 0.8107 (mm-40) REVERT: L 79 GLU cc_start: 0.8575 (tp30) cc_final: 0.8142 (tp30) REVERT: A 69 TRP cc_start: 0.7159 (m-90) cc_final: 0.6932 (m-90) REVERT: A 475 MET cc_start: 0.8438 (mmm) cc_final: 0.8114 (mmt) REVERT: E 632 ASP cc_start: 0.8806 (t70) cc_final: 0.8376 (t0) REVERT: F 5 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8732 (mm) REVERT: F 23 GLU cc_start: 0.7886 (mp0) cc_final: 0.7671 (mp0) REVERT: F 82 LYS cc_start: 0.8217 (tttp) cc_final: 0.7899 (ttmm) REVERT: F 98 ASP cc_start: 0.8936 (m-30) cc_final: 0.8021 (t0) REVERT: I 1 ASP cc_start: 0.7967 (p0) cc_final: 0.7715 (p0) REVERT: I 5 THR cc_start: 0.7977 (m) cc_final: 0.7530 (p) REVERT: I 24 GLN cc_start: 0.8311 (mt0) cc_final: 0.7958 (mp10) REVERT: I 55 GLU cc_start: 0.8353 (tp30) cc_final: 0.8136 (tp30) REVERT: I 58 VAL cc_start: 0.8682 (t) cc_final: 0.8345 (p) REVERT: I 77 ASN cc_start: 0.8615 (t0) cc_final: 0.8365 (t0) REVERT: J 86 ASP cc_start: 0.8389 (t0) cc_final: 0.8164 (t0) REVERT: K 79 GLU cc_start: 0.8625 (tp30) cc_final: 0.8079 (tp30) REVERT: K 90 MET cc_start: 0.9130 (tpp) cc_final: 0.8820 (tpp) REVERT: M 69 TRP cc_start: 0.7270 (m-90) cc_final: 0.6800 (m-90) REVERT: N 542 ARG cc_start: 0.9136 (ttm170) cc_final: 0.8856 (ttp-170) REVERT: N 621 GLU cc_start: 0.9038 (pt0) cc_final: 0.8603 (pp20) REVERT: N 632 ASP cc_start: 0.8944 (t70) cc_final: 0.8396 (t0) REVERT: O 30 ARG cc_start: 0.8340 (mtt90) cc_final: 0.8133 (mtt90) REVERT: O 84 SER cc_start: 0.9325 (m) cc_final: 0.9033 (t) REVERT: P 5 THR cc_start: 0.7783 (m) cc_final: 0.7461 (p) REVERT: P 55 GLU cc_start: 0.8206 (tp30) cc_final: 0.7894 (tp30) REVERT: P 58 VAL cc_start: 0.8579 (t) cc_final: 0.8156 (p) REVERT: P 77 ASN cc_start: 0.8193 (t0) cc_final: 0.7886 (t0) REVERT: Q 5 GLN cc_start: 0.9293 (tp-100) cc_final: 0.9055 (tp-100) REVERT: Q 27 ASP cc_start: 0.6208 (t0) cc_final: 0.5742 (t0) REVERT: Q 32 TYR cc_start: 0.8605 (m-10) cc_final: 0.8170 (m-10) REVERT: R 20 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7558 (mpp80) REVERT: R 70 ARG cc_start: 0.7675 (mmm160) cc_final: 0.7402 (mmp-170) REVERT: R 79 GLU cc_start: 0.8668 (tp30) cc_final: 0.8157 (tp30) outliers start: 61 outliers final: 56 residues processed: 324 average time/residue: 0.4218 time to fit residues: 210.5505 Evaluate side-chains 322 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 264 time to evaluate : 3.065 ------------------------------------------------------------------------------- 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 499 THR 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 7 TYR 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 242 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 7 TYR 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 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 488 VAL Chi-restraints excluded: chain N residue 626 MET 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 17 ASP 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: 8.9990 chunk 240 optimal weight: 0.9980 chunk 272 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 167 optimal weight: 0.2980 chunk 173 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.084715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.059052 restraints weight = 63065.346| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.42 r_work: 0.2815 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26835 Z= 0.119 Angle : 0.564 10.341 36699 Z= 0.268 Chirality : 0.043 0.284 4374 Planarity : 0.003 0.044 4440 Dihedral : 7.348 80.000 6087 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.32 % Allowed : 15.79 % Favored : 81.89 % 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: -0.96 (0.16), residues: 3021 helix: 0.39 (0.30), residues: 369 sheet: 0.03 (0.18), residues: 906 loop : -1.26 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 69 HIS 0.001 0.000 HIS A 330 PHE 0.008 0.001 PHE G 53 TYR 0.010 0.001 TYR D 91 ARG 0.010 0.000 ARG M 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 63) link_NAG-ASN : angle 1.57854 ( 189) link_ALPHA1-6 : bond 0.00748 ( 15) link_ALPHA1-6 : angle 1.44801 ( 45) link_BETA1-4 : bond 0.00471 ( 36) link_BETA1-4 : angle 1.49588 ( 108) link_ALPHA1-2 : bond 0.00579 ( 9) link_ALPHA1-2 : angle 1.50887 ( 27) link_ALPHA1-3 : bond 0.01017 ( 12) link_ALPHA1-3 : angle 1.40048 ( 36) hydrogen bonds : bond 0.02672 ( 480) hydrogen bonds : angle 4.59258 ( 1224) SS BOND : bond 0.00342 ( 45) SS BOND : angle 0.79941 ( 90) covalent geometry : bond 0.00281 (26655) covalent geometry : angle 0.54337 (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 330 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 268 time to evaluate : 3.223 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: 0.7157 (m-90) cc_final: 0.6840 (m-90) REVERT: G 271 MET cc_start: 0.8739 (tpt) cc_final: 0.8426 (mmp) REVERT: B 632 ASP cc_start: 0.9035 (t70) cc_final: 0.8553 (t0) REVERT: C 30 ARG cc_start: 0.8310 (mtt90) cc_final: 0.7868 (mtt180) REVERT: C 53 LYS cc_start: 0.9541 (ttmt) cc_final: 0.9267 (ttmm) REVERT: D 5 THR cc_start: 0.7653 (m) cc_final: 0.7354 (p) REVERT: D 55 GLU cc_start: 0.8286 (tp30) cc_final: 0.7942 (tp30) REVERT: D 58 VAL cc_start: 0.8528 (t) cc_final: 0.8122 (p) REVERT: D 60 SER cc_start: 0.8594 (t) cc_final: 0.8343 (m) REVERT: D 77 ASN cc_start: 0.8462 (t0) cc_final: 0.8224 (t0) REVERT: L 26 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8082 (mm-40) REVERT: L 79 GLU cc_start: 0.8567 (tp30) cc_final: 0.8140 (tp30) REVERT: E 632 ASP cc_start: 0.8794 (t70) cc_final: 0.8359 (t0) REVERT: F 5 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8720 (mm) REVERT: F 23 GLU cc_start: 0.7889 (mp0) cc_final: 0.7661 (mp0) REVERT: F 82 LYS cc_start: 0.8228 (tttp) cc_final: 0.7907 (ttmm) REVERT: F 98 ASP cc_start: 0.8936 (m-30) cc_final: 0.8080 (t0) REVERT: I 5 THR cc_start: 0.7899 (m) cc_final: 0.7476 (p) REVERT: I 24 GLN cc_start: 0.8319 (mt0) cc_final: 0.7957 (mp10) REVERT: I 58 VAL cc_start: 0.8636 (t) cc_final: 0.8302 (p) REVERT: I 77 ASN cc_start: 0.8566 (t0) cc_final: 0.8272 (t0) REVERT: J 86 ASP cc_start: 0.8391 (t0) cc_final: 0.8179 (t0) REVERT: K 26 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8166 (tp-100) REVERT: K 79 GLU cc_start: 0.8620 (tp30) cc_final: 0.8075 (tp30) REVERT: K 90 MET cc_start: 0.9126 (tpp) cc_final: 0.8822 (tpp) REVERT: M 69 TRP cc_start: 0.7260 (m-90) cc_final: 0.6796 (m-90) REVERT: N 542 ARG cc_start: 0.9171 (ttm170) cc_final: 0.8889 (ttp-170) REVERT: N 621 GLU cc_start: 0.9048 (pt0) cc_final: 0.8614 (pp20) REVERT: N 632 ASP cc_start: 0.8953 (t70) cc_final: 0.8414 (t0) REVERT: O 30 ARG cc_start: 0.8339 (mtt90) cc_final: 0.8059 (mtm-85) REVERT: O 84 SER cc_start: 0.9323 (m) cc_final: 0.9025 (t) REVERT: P 5 THR cc_start: 0.7738 (m) cc_final: 0.7448 (p) REVERT: P 55 GLU cc_start: 0.8203 (tp30) cc_final: 0.7905 (tp30) REVERT: P 58 VAL cc_start: 0.8558 (t) cc_final: 0.8134 (p) REVERT: P 77 ASN cc_start: 0.8227 (t0) cc_final: 0.7928 (t0) REVERT: Q 5 GLN cc_start: 0.9274 (tp-100) cc_final: 0.9033 (tp-100) REVERT: Q 27 ASP cc_start: 0.6253 (t0) cc_final: 0.5790 (t0) REVERT: Q 32 TYR cc_start: 0.8584 (m-10) cc_final: 0.8150 (m-10) REVERT: R 20 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7570 (mpp80) REVERT: R 70 ARG cc_start: 0.7701 (mmm160) cc_final: 0.7420 (mmp-170) REVERT: R 79 GLU cc_start: 0.8599 (tp30) cc_final: 0.8109 (tp30) outliers start: 62 outliers final: 54 residues processed: 320 average time/residue: 0.4154 time to fit residues: 204.6582 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 : 3.178 ------------------------------------------------------------------------------- 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 499 THR 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 7 TYR 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 242 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 425 ASN 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 K residue 7 TYR 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 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 488 VAL Chi-restraints excluded: chain N residue 626 MET Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain P residue 17 ASP 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 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 86 optimal weight: 7.9990 chunk 270 optimal weight: 0.6980 chunk 176 optimal weight: 4.9990 chunk 258 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 227 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 287 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.084552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.058904 restraints weight = 62795.132| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.41 r_work: 0.2813 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 26835 Z= 0.167 Angle : 0.686 59.193 36699 Z= 0.363 Chirality : 0.044 0.480 4374 Planarity : 0.004 0.062 4440 Dihedral : 7.366 80.024 6087 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.17 % Allowed : 16.09 % Favored : 81.74 % 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: -1.02 (0.15), residues: 3021 helix: 0.24 (0.29), residues: 381 sheet: 0.04 (0.18), residues: 906 loop : -1.31 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 69 HIS 0.001 0.000 HIS G 72 PHE 0.009 0.001 PHE G 53 TYR 0.011 0.001 TYR D 91 ARG 0.009 0.000 ARG M 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 63) link_NAG-ASN : angle 1.58462 ( 189) link_ALPHA1-6 : bond 0.00754 ( 15) link_ALPHA1-6 : angle 1.44230 ( 45) link_BETA1-4 : bond 0.00488 ( 36) link_BETA1-4 : angle 1.50681 ( 108) link_ALPHA1-2 : bond 0.00590 ( 9) link_ALPHA1-2 : angle 1.48973 ( 27) link_ALPHA1-3 : bond 0.01024 ( 12) link_ALPHA1-3 : angle 1.39868 ( 36) hydrogen bonds : bond 0.02730 ( 480) hydrogen bonds : angle 4.59549 ( 1224) SS BOND : bond 0.00357 ( 45) SS BOND : angle 0.79352 ( 90) covalent geometry : bond 0.00375 (26655) covalent geometry : angle 0.67067 (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 320 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 262 time to evaluate : 3.084 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: 0.7162 (m-90) cc_final: 0.6839 (m-90) REVERT: G 271 MET cc_start: 0.8738 (tpt) cc_final: 0.8427 (mmp) REVERT: B 632 ASP cc_start: 0.9039 (t70) cc_final: 0.8558 (t0) REVERT: C 30 ARG cc_start: 0.8311 (mtt90) cc_final: 0.7863 (mtt180) REVERT: C 53 LYS cc_start: 0.9543 (ttmt) cc_final: 0.9266 (ttmm) REVERT: D 5 THR cc_start: 0.7663 (m) cc_final: 0.7364 (p) REVERT: D 55 GLU cc_start: 0.8283 (tp30) cc_final: 0.7941 (tp30) REVERT: D 58 VAL cc_start: 0.8534 (t) cc_final: 0.8129 (p) REVERT: D 60 SER cc_start: 0.8599 (t) cc_final: 0.8348 (m) REVERT: D 77 ASN cc_start: 0.8459 (t0) cc_final: 0.8224 (t0) REVERT: L 26 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8084 (mm-40) REVERT: L 79 GLU cc_start: 0.8574 (tp30) cc_final: 0.8147 (tp30) REVERT: E 632 ASP cc_start: 0.8797 (t70) cc_final: 0.8364 (t0) REVERT: F 5 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8722 (mm) REVERT: F 23 GLU cc_start: 0.7899 (mp0) cc_final: 0.7679 (mp0) REVERT: F 82 LYS cc_start: 0.8231 (tttp) cc_final: 0.7909 (ttmm) REVERT: F 98 ASP cc_start: 0.8946 (m-30) cc_final: 0.8093 (t0) REVERT: I 5 THR cc_start: 0.7899 (m) cc_final: 0.7490 (p) REVERT: I 24 GLN cc_start: 0.8324 (mt0) cc_final: 0.7960 (mp10) REVERT: I 58 VAL cc_start: 0.8640 (t) cc_final: 0.8302 (p) REVERT: K 26 GLN cc_start: 0.8404 (mm-40) cc_final: 0.7961 (tp-100) REVERT: K 70 ARG cc_start: 0.7414 (mmm160) cc_final: 0.6880 (mmp-170) REVERT: K 79 GLU cc_start: 0.8629 (tp30) cc_final: 0.8083 (tp30) REVERT: K 90 MET cc_start: 0.9130 (tpp) cc_final: 0.8853 (tpp) REVERT: M 69 TRP cc_start: 0.7264 (m-90) cc_final: 0.6796 (m-90) REVERT: N 542 ARG cc_start: 0.9169 (ttm170) cc_final: 0.8891 (ttp-170) REVERT: N 621 GLU cc_start: 0.9047 (pt0) cc_final: 0.8613 (pp20) REVERT: N 632 ASP cc_start: 0.8949 (t70) cc_final: 0.8410 (t0) REVERT: O 30 ARG cc_start: 0.8341 (mtt90) cc_final: 0.8061 (mtm-85) REVERT: O 84 SER cc_start: 0.9323 (m) cc_final: 0.9026 (t) REVERT: P 5 THR cc_start: 0.7745 (m) cc_final: 0.7458 (p) REVERT: P 55 GLU cc_start: 0.8199 (tp30) cc_final: 0.7900 (tp30) REVERT: P 58 VAL cc_start: 0.8560 (t) cc_final: 0.8136 (p) REVERT: P 77 ASN cc_start: 0.8226 (t0) cc_final: 0.7928 (t0) REVERT: Q 5 GLN cc_start: 0.9275 (tp-100) cc_final: 0.9030 (tp-100) REVERT: Q 27 ASP cc_start: 0.6321 (t0) cc_final: 0.5864 (t0) REVERT: Q 32 TYR cc_start: 0.8587 (m-10) cc_final: 0.8151 (m-10) REVERT: R 20 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7571 (mpp80) REVERT: R 70 ARG cc_start: 0.7699 (mmm160) cc_final: 0.7409 (mmp-170) REVERT: R 79 GLU cc_start: 0.8601 (tp30) cc_final: 0.8112 (tp30) outliers start: 58 outliers final: 54 residues processed: 312 average time/residue: 0.4134 time to fit residues: 198.7321 Evaluate side-chains 316 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 260 time to evaluate : 3.138 ------------------------------------------------------------------------------- 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 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 7 TYR 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 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 K residue 7 TYR 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 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 488 VAL Chi-restraints excluded: chain N residue 626 MET Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain P residue 17 ASP 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 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 66 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 200 optimal weight: 0.6980 chunk 124 optimal weight: 0.4980 chunk 221 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 215 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 294 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3480 r_free = 0.3480 target = 0.084552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.058898 restraints weight = 63077.887| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.42 r_work: 0.2812 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.004 0.097 26835 Z= 0.168 Angle : 0.687 59.193 36699 Z= 0.363 Chirality : 0.044 0.480 4374 Planarity : 0.004 0.062 4440 Dihedral : 7.366 80.024 6087 Min Nonbonded Distance : 1.554 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.10 % Allowed : 16.24 % Favored : 81.66 % 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: -1.02 (0.15), residues: 3021 helix: 0.24 (0.29), residues: 381 sheet: 0.04 (0.18), residues: 906 loop : -1.31 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 69 HIS 0.001 0.000 HIS G 72 PHE 0.009 0.001 PHE G 53 TYR 0.011 0.001 TYR D 91 ARG 0.009 0.000 ARG M 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 63) link_NAG-ASN : angle 1.58462 ( 189) link_ALPHA1-6 : bond 0.00754 ( 15) link_ALPHA1-6 : angle 1.44230 ( 45) link_BETA1-4 : bond 0.00488 ( 36) link_BETA1-4 : angle 1.50681 ( 108) link_ALPHA1-2 : bond 0.00590 ( 9) link_ALPHA1-2 : angle 1.48973 ( 27) link_ALPHA1-3 : bond 0.01024 ( 12) link_ALPHA1-3 : angle 1.39868 ( 36) hydrogen bonds : bond 0.02730 ( 480) hydrogen bonds : angle 4.59549 ( 1224) SS BOND : bond 0.00885 ( 45) SS BOND : angle 0.87171 ( 90) covalent geometry : bond 0.00375 (26655) covalent geometry : angle 0.67069 (36204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12596.10 seconds wall clock time: 217 minutes 46.15 seconds (13066.15 seconds total)