Starting phenix.real_space_refine on Fri Sep 19 12:49:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bew_44484/09_2025/9bew_44484.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bew_44484/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bew_44484/09_2025/9bew_44484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bew_44484/09_2025/9bew_44484.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bew_44484/09_2025/9bew_44484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bew_44484/09_2025/9bew_44484.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 6.96, per 1000 atoms: 0.27 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: 2.61 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.01 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: 5.92 Time building geometry restraints manager: 3.44 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: 0.07 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: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.240 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.740 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.001 0.000 ARG H 71 TYR 0.009 0.001 TYR D 91 PHE 0.010 0.001 PHE M 53 TRP 0.007 0.001 TRP O 50 HIS 0.003 0.001 HIS E 564 Details of bonding type rmsd covalent geometry : bond 0.00442 (26655) covalent geometry : angle 0.72903 (36204) SS BOND : bond 0.00442 ( 45) SS BOND : angle 1.58804 ( 90) hydrogen bonds : bond 0.28237 ( 480) hydrogen bonds : angle 9.62453 ( 1224) 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) 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_NAG-ASN : bond 0.00274 ( 63) link_NAG-ASN : angle 1.67442 ( 189) *********************** 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 : 0.862 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: 0.8385 (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: 0.7659 (mm-40) REVERT: H 32 TYR cc_start: 0.8209 (m-10) cc_final: 0.7986 (m-10) REVERT: H 90 TYR cc_start: 0.7983 (m-10) cc_final: 0.7736 (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: 0.8262 (tp30) REVERT: M 56 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8579 (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: 0.7973 (mm-40) REVERT: Q 46 GLU cc_start: 0.8262 (tt0) cc_final: 0.7903 (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: 0.8100 (mp10) REVERT: R 79 GLU cc_start: 0.8732 (tp30) cc_final: 0.8277 (tp30) outliers start: 27 outliers final: 3 residues processed: 458 average time/residue: 0.2434 time to fit residues: 159.0319 Evaluate side-chains 295 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 291 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.0170 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 overall best weight: 2.6024 ------------------------------------------------------------------------------- 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 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 3 GLN J 31 ASN 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 38 GLN P 69 GLN Q 3 GLN Q 31 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.083853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.057574 restraints weight = 63714.157| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.66 r_work: 0.2770 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 26835 Z= 0.240 Angle : 0.683 9.611 36699 Z= 0.324 Chirality : 0.048 0.339 4374 Planarity : 0.004 0.064 4440 Dihedral : 11.012 87.537 6091 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.16 % Favored : 94.77 % Rotamer: Outliers : 1.16 % Allowed : 10.42 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.89 (0.13), residues: 3021 helix: -2.56 (0.20), residues: 384 sheet: -1.51 (0.15), residues: 903 loop : -2.00 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 96 TYR 0.013 0.001 TYR E 638 PHE 0.013 0.002 PHE G 53 TRP 0.019 0.002 TRP A 69 HIS 0.003 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00555 (26655) covalent geometry : angle 0.64826 (36204) SS BOND : bond 0.00379 ( 45) SS BOND : angle 1.00585 ( 90) hydrogen bonds : bond 0.04560 ( 480) hydrogen bonds : angle 6.27722 ( 1224) link_ALPHA1-2 : bond 0.00870 ( 9) link_ALPHA1-2 : angle 1.55027 ( 27) link_ALPHA1-3 : bond 0.01253 ( 12) link_ALPHA1-3 : angle 1.89157 ( 36) link_ALPHA1-6 : bond 0.00783 ( 15) link_ALPHA1-6 : angle 2.19381 ( 45) link_BETA1-4 : bond 0.00685 ( 36) link_BETA1-4 : angle 2.56506 ( 108) link_NAG-ASN : bond 0.00335 ( 63) link_NAG-ASN : angle 1.94492 ( 189) *********************** 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 318 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 287 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 271 MET cc_start: 0.8491 (tpt) cc_final: 0.8270 (mmp) REVERT: G 475 MET cc_start: 0.8348 (mmm) cc_final: 0.7944 (mmm) REVERT: B 632 ASP cc_start: 0.9026 (t70) cc_final: 0.8541 (t0) REVERT: C 30 ARG cc_start: 0.8198 (mtt90) cc_final: 0.7848 (mtt90) REVERT: C 53 LYS cc_start: 0.9436 (ttmt) cc_final: 0.9098 (ttmm) REVERT: C 82 LYS cc_start: 0.7968 (tttp) cc_final: 0.7702 (ttmm) REVERT: C 98 ASP cc_start: 0.9029 (m-30) cc_final: 0.8143 (t0) REVERT: D 77 ASN cc_start: 0.8350 (t0) cc_final: 0.7955 (t0) REVERT: H 54 ARG cc_start: 0.8507 (mtt90) cc_final: 0.7960 (mmp80) REVERT: H 86 ASP cc_start: 0.8405 (t0) cc_final: 0.8115 (t0) REVERT: H 90 TYR cc_start: 0.7840 (m-10) cc_final: 0.7597 (m-10) REVERT: L 66 ASP cc_start: 0.7856 (t0) cc_final: 0.7099 (t0) REVERT: L 79 GLU cc_start: 0.8461 (tp30) cc_final: 0.8120 (tp30) REVERT: A 475 MET cc_start: 0.8338 (mmm) cc_final: 0.7809 (mmm) REVERT: E 584 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8015 (mt-10) REVERT: E 621 GLU cc_start: 0.8758 (pt0) cc_final: 0.8285 (pt0) REVERT: E 632 ASP cc_start: 0.9014 (t70) cc_final: 0.8583 (t0) REVERT: F 31 ASP cc_start: 0.9270 (m-30) cc_final: 0.9069 (m-30) REVERT: F 53 LYS cc_start: 0.9414 (ttmt) cc_final: 0.9045 (ttmm) REVERT: F 82 LYS cc_start: 0.7916 (tttp) cc_final: 0.7643 (ttmm) REVERT: F 98 ASP cc_start: 0.8958 (m-30) cc_final: 0.8049 (t0) REVERT: F 100 ASP cc_start: 0.8513 (m-30) cc_final: 0.7724 (p0) REVERT: I 24 GLN cc_start: 0.8282 (mt0) cc_final: 0.8031 (mp10) REVERT: I 58 VAL cc_start: 0.8681 (t) cc_final: 0.8350 (p) REVERT: J 54 ARG cc_start: 0.8554 (mtt90) cc_final: 0.7978 (mmp80) REVERT: K 66 ASP cc_start: 0.7852 (t0) cc_final: 0.7339 (t0) REVERT: K 79 GLU cc_start: 0.8614 (tp30) cc_final: 0.8039 (tp30) REVERT: M 69 TRP cc_start: 0.7231 (m-90) cc_final: 0.6534 (m-90) REVERT: M 475 MET cc_start: 0.8303 (tpp) cc_final: 0.8067 (mmm) REVERT: N 542 ARG cc_start: 0.9085 (ttm170) cc_final: 0.8743 (ttp-170) REVERT: N 632 ASP cc_start: 0.9054 (t70) cc_final: 0.8539 (t0) REVERT: O 82 LYS cc_start: 0.7984 (tttp) cc_final: 0.7770 (ttmm) REVERT: O 84 SER cc_start: 0.9270 (m) cc_final: 0.9029 (t) REVERT: O 98 ASP cc_start: 0.8990 (m-30) cc_final: 0.8128 (t0) REVERT: P 55 GLU cc_start: 0.7768 (tp30) cc_final: 0.7324 (tp30) REVERT: P 77 ASN cc_start: 0.8091 (t0) cc_final: 0.7626 (t0) REVERT: Q 27 ASP cc_start: 0.7451 (t0) cc_final: 0.7206 (t0) REVERT: Q 32 TYR cc_start: 0.8432 (m-10) cc_final: 0.8188 (m-10) REVERT: Q 46 GLU cc_start: 0.8441 (tt0) cc_final: 0.8138 (tt0) REVERT: Q 54 ARG cc_start: 0.8631 (mtt90) cc_final: 0.8002 (mmp80) REVERT: Q 86 ASP cc_start: 0.8437 (t0) cc_final: 0.8187 (t0) REVERT: Q 90 TYR cc_start: 0.7782 (m-10) cc_final: 0.7512 (m-10) REVERT: R 42 GLN cc_start: 0.8755 (tp40) cc_final: 0.7947 (mp10) REVERT: R 79 GLU cc_start: 0.8643 (tp30) cc_final: 0.8100 (tp30) outliers start: 31 outliers final: 21 residues processed: 313 average time/residue: 0.2074 time to fit residues: 97.4761 Evaluate side-chains 298 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 277 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 E residue 620 SER Chi-restraints excluded: chain I residue 22 THR 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 R residue 85 ASP Chi-restraints excluded: chain R residue 92 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 224 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 202 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 219 optimal weight: 3.9990 chunk 254 optimal weight: 0.0770 chunk 81 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 overall best weight: 2.1744 ------------------------------------------------------------------------------- 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 I 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.082963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.056711 restraints weight = 63833.829| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.66 r_work: 0.2749 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26835 Z= 0.197 Angle : 0.610 9.840 36699 Z= 0.292 Chirality : 0.045 0.302 4374 Planarity : 0.004 0.053 4440 Dihedral : 9.529 85.994 6087 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.76 % Allowed : 12.67 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.14), residues: 3021 helix: -1.57 (0.25), residues: 381 sheet: -1.23 (0.16), residues: 861 loop : -1.81 (0.13), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 56 TYR 0.011 0.001 TYR I 91 PHE 0.011 0.001 PHE G 53 TRP 0.018 0.001 TRP A 69 HIS 0.002 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00459 (26655) covalent geometry : angle 0.57905 (36204) SS BOND : bond 0.00419 ( 45) SS BOND : angle 1.20506 ( 90) hydrogen bonds : bond 0.04105 ( 480) hydrogen bonds : angle 5.57002 ( 1224) link_ALPHA1-2 : bond 0.00562 ( 9) link_ALPHA1-2 : angle 2.12023 ( 27) link_ALPHA1-3 : bond 0.01080 ( 12) link_ALPHA1-3 : angle 1.78317 ( 36) link_ALPHA1-6 : bond 0.00745 ( 15) link_ALPHA1-6 : angle 1.69280 ( 45) link_BETA1-4 : bond 0.00577 ( 36) link_BETA1-4 : angle 1.87718 ( 108) link_NAG-ASN : bond 0.00261 ( 63) link_NAG-ASN : angle 1.82401 ( 189) *********************** 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 329 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 282 time to evaluate : 1.083 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: 0.6927 (m-90) cc_final: 0.6182 (m-90) REVERT: G 205 CYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7953 (m) REVERT: G 271 MET cc_start: 0.8510 (tpt) cc_final: 0.8268 (mmp) REVERT: G 475 MET cc_start: 0.8298 (mmm) cc_final: 0.8017 (mmm) REVERT: B 632 ASP cc_start: 0.9075 (t70) cc_final: 0.8614 (t0) REVERT: C 23 GLU cc_start: 0.7551 (mp0) cc_final: 0.7349 (mp0) REVERT: C 30 ARG cc_start: 0.8217 (mtt90) cc_final: 0.7937 (mtt90) REVERT: C 53 LYS cc_start: 0.9440 (ttmt) cc_final: 0.9100 (ttmm) REVERT: C 82 LYS cc_start: 0.7950 (tttp) cc_final: 0.7705 (ttmm) REVERT: C 98 ASP cc_start: 0.8961 (m-30) cc_final: 0.7991 (t0) REVERT: D 77 ASN cc_start: 0.8391 (t0) cc_final: 0.8009 (t0) REVERT: H 54 ARG cc_start: 0.8588 (mtt90) cc_final: 0.8060 (mmp80) REVERT: H 86 ASP cc_start: 0.8533 (t0) cc_final: 0.8185 (t0) REVERT: H 90 TYR cc_start: 0.7869 (m-10) cc_final: 0.7587 (m-10) REVERT: L 66 ASP cc_start: 0.7979 (t0) cc_final: 0.7239 (t0) REVERT: L 70 ARG cc_start: 0.7374 (mmp-170) cc_final: 0.7150 (mmp-170) REVERT: L 79 GLU cc_start: 0.8472 (tp30) cc_final: 0.8147 (tp30) REVERT: A 161 MET cc_start: 0.8503 (tpt) cc_final: 0.8213 (mmm) REVERT: A 475 MET cc_start: 0.8403 (mmm) cc_final: 0.7816 (mmm) REVERT: E 584 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7975 (mt-10) REVERT: E 632 ASP cc_start: 0.9009 (t70) cc_final: 0.8590 (t0) REVERT: E 634 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8318 (mt-10) REVERT: F 23 GLU cc_start: 0.7708 (mp0) cc_final: 0.7460 (mp0) REVERT: F 31 ASP cc_start: 0.9319 (m-30) cc_final: 0.9107 (m-30) REVERT: F 53 LYS cc_start: 0.9437 (ttmt) cc_final: 0.9016 (ttmm) REVERT: F 82 LYS cc_start: 0.7899 (tttp) cc_final: 0.7624 (ttmm) REVERT: F 98 ASP cc_start: 0.8955 (m-30) cc_final: 0.7971 (t0) REVERT: F 100 ASP cc_start: 0.8487 (m-30) cc_final: 0.7797 (p0) REVERT: I 24 GLN cc_start: 0.8222 (mt0) cc_final: 0.7928 (mp10) REVERT: I 55 GLU cc_start: 0.8371 (tp30) cc_final: 0.8168 (tp30) REVERT: I 58 VAL cc_start: 0.8618 (t) cc_final: 0.8285 (p) REVERT: I 77 ASN cc_start: 0.8700 (t0) cc_final: 0.8476 (t0) REVERT: I 103 ARG cc_start: 0.8259 (ptt180) cc_final: 0.7961 (ttp-110) REVERT: J 54 ARG cc_start: 0.8550 (mtt90) cc_final: 0.8120 (mmp80) REVERT: K 66 ASP cc_start: 0.7849 (t0) cc_final: 0.7412 (t0) REVERT: K 79 GLU cc_start: 0.8574 (tp30) cc_final: 0.8009 (tp30) REVERT: K 90 MET cc_start: 0.8982 (tpp) cc_final: 0.8756 (tpp) REVERT: M 69 TRP cc_start: 0.7245 (m-90) cc_final: 0.6469 (m-90) REVERT: M 205 CYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7847 (m) REVERT: N 542 ARG cc_start: 0.9160 (ttm170) cc_final: 0.8775 (ttp-170) REVERT: N 632 ASP cc_start: 0.9038 (t70) cc_final: 0.8506 (t0) REVERT: O 82 LYS cc_start: 0.7928 (tttp) cc_final: 0.7626 (ttmm) REVERT: O 84 SER cc_start: 0.9322 (m) cc_final: 0.9072 (t) REVERT: O 98 ASP cc_start: 0.8941 (m-30) cc_final: 0.8010 (t0) REVERT: O 100 ASP cc_start: 0.8417 (m-30) cc_final: 0.7646 (p0) REVERT: P 55 GLU cc_start: 0.8098 (tp30) cc_final: 0.7726 (tp30) REVERT: P 77 ASN cc_start: 0.8068 (t0) cc_final: 0.7704 (t0) REVERT: P 103 ARG cc_start: 0.8170 (ptt180) cc_final: 0.7887 (ttp-110) REVERT: Q 32 TYR cc_start: 0.8589 (m-10) cc_final: 0.8379 (m-10) REVERT: Q 86 ASP cc_start: 0.8424 (t0) cc_final: 0.8175 (t0) REVERT: Q 90 TYR cc_start: 0.7804 (m-10) cc_final: 0.7534 (m-10) REVERT: R 26 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7767 (mm-40) REVERT: R 79 GLU cc_start: 0.8604 (tp30) cc_final: 0.8086 (tp30) outliers start: 47 outliers final: 37 residues processed: 322 average time/residue: 0.2096 time to fit residues: 101.9969 Evaluate side-chains 314 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 275 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 123 THR 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 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 371 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 499 THR 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 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 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 O residue 31 ASP Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 22 optimal weight: 4.9990 chunk 168 optimal weight: 0.0040 chunk 24 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 294 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.084528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.058440 restraints weight = 62761.840| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.64 r_work: 0.2792 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26835 Z= 0.103 Angle : 0.542 9.777 36699 Z= 0.257 Chirality : 0.044 0.269 4374 Planarity : 0.003 0.040 4440 Dihedral : 8.321 83.557 6087 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.54 % Allowed : 13.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.15), residues: 3021 helix: -0.80 (0.27), residues: 369 sheet: -0.76 (0.17), residues: 897 loop : -1.50 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 56 TYR 0.009 0.001 TYR O 90 PHE 0.006 0.001 PHE M 53 TRP 0.017 0.001 TRP A 69 HIS 0.002 0.000 HIS R 38 Details of bonding type rmsd covalent geometry : bond 0.00231 (26655) covalent geometry : angle 0.51644 (36204) SS BOND : bond 0.00388 ( 45) SS BOND : angle 0.77881 ( 90) hydrogen bonds : bond 0.02973 ( 480) hydrogen bonds : angle 5.17877 ( 1224) link_ALPHA1-2 : bond 0.00655 ( 9) link_ALPHA1-2 : angle 1.43367 ( 27) link_ALPHA1-3 : bond 0.01142 ( 12) link_ALPHA1-3 : angle 1.62660 ( 36) link_ALPHA1-6 : bond 0.00892 ( 15) link_ALPHA1-6 : angle 1.52645 ( 45) link_BETA1-4 : bond 0.00475 ( 36) link_BETA1-4 : angle 1.68013 ( 108) link_NAG-ASN : bond 0.00221 ( 63) link_NAG-ASN : angle 1.61894 ( 189) *********************** 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 339 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 298 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 69 TRP cc_start: 0.7024 (m-90) cc_final: 0.6431 (m-90) REVERT: G 205 CYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7895 (m) REVERT: G 271 MET cc_start: 0.8492 (tpt) cc_final: 0.8199 (mmp) REVERT: B 632 ASP cc_start: 0.8987 (t70) cc_final: 0.8566 (t0) REVERT: B 634 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8259 (mp0) REVERT: C 30 ARG cc_start: 0.8167 (mtt90) cc_final: 0.7965 (mtt90) REVERT: C 53 LYS cc_start: 0.9428 (ttmt) cc_final: 0.9122 (ttmm) REVERT: C 82 LYS cc_start: 0.7983 (tttp) cc_final: 0.7744 (ttmm) REVERT: C 98 ASP cc_start: 0.8932 (m-30) cc_final: 0.7950 (t0) REVERT: D 5 THR cc_start: 0.7843 (m) cc_final: 0.7547 (p) REVERT: D 77 ASN cc_start: 0.8383 (t0) cc_final: 0.7883 (t0) REVERT: H 54 ARG cc_start: 0.8507 (mtt90) cc_final: 0.8037 (mmp80) REVERT: H 86 ASP cc_start: 0.8479 (t0) cc_final: 0.8109 (t0) REVERT: H 90 TYR cc_start: 0.7667 (m-10) cc_final: 0.7385 (m-10) REVERT: L 66 ASP cc_start: 0.7980 (t0) cc_final: 0.7702 (t0) REVERT: L 70 ARG cc_start: 0.7376 (mmp-170) cc_final: 0.7154 (mmp-170) REVERT: L 79 GLU cc_start: 0.8447 (tp30) cc_final: 0.8071 (tp30) REVERT: A 475 MET cc_start: 0.8313 (mmm) cc_final: 0.7694 (mmm) REVERT: E 584 GLU cc_start: 0.8523 (mt-10) cc_final: 0.7890 (mt-10) REVERT: E 632 ASP cc_start: 0.8948 (t70) cc_final: 0.8521 (t0) REVERT: F 23 GLU cc_start: 0.7705 (mp0) cc_final: 0.7415 (mp0) REVERT: F 53 LYS cc_start: 0.9444 (ttmt) cc_final: 0.9070 (ttmm) REVERT: F 82 LYS cc_start: 0.7910 (tttp) cc_final: 0.7573 (ttmm) REVERT: F 98 ASP cc_start: 0.8927 (m-30) cc_final: 0.7851 (t0) REVERT: F 100 ASP cc_start: 0.8358 (m-30) cc_final: 0.7688 (p0) REVERT: I 5 THR cc_start: 0.8078 (m) cc_final: 0.7513 (p) REVERT: I 24 GLN cc_start: 0.8201 (mt0) cc_final: 0.7859 (mp10) REVERT: I 55 GLU cc_start: 0.8392 (tp30) cc_final: 0.8139 (tp30) REVERT: I 58 VAL cc_start: 0.8605 (t) cc_final: 0.8291 (p) REVERT: I 77 ASN cc_start: 0.8699 (t0) cc_final: 0.8428 (t0) REVERT: I 103 ARG cc_start: 0.8231 (ptt180) cc_final: 0.7938 (ttp-110) REVERT: J 54 ARG cc_start: 0.8575 (mtt90) cc_final: 0.8116 (mmp80) REVERT: J 86 ASP cc_start: 0.8405 (t0) cc_final: 0.8152 (t0) REVERT: K 66 ASP cc_start: 0.7866 (t0) cc_final: 0.7341 (t0) REVERT: K 79 GLU cc_start: 0.8572 (tp30) cc_final: 0.8004 (tp30) REVERT: K 90 MET cc_start: 0.8997 (tpp) cc_final: 0.8663 (tpp) REVERT: M 69 TRP cc_start: 0.7121 (m-90) cc_final: 0.6416 (m-90) REVERT: M 205 CYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7797 (m) REVERT: M 475 MET cc_start: 0.8473 (mmm) cc_final: 0.7867 (mmm) REVERT: N 542 ARG cc_start: 0.9082 (ttm170) cc_final: 0.8675 (ttp-170) REVERT: N 621 GLU cc_start: 0.9207 (pt0) cc_final: 0.8518 (pp20) REVERT: N 632 ASP cc_start: 0.8925 (t70) cc_final: 0.8377 (t0) REVERT: O 30 ARG cc_start: 0.8280 (mtt90) cc_final: 0.7993 (mtt90) REVERT: O 82 LYS cc_start: 0.7938 (tttp) cc_final: 0.7647 (ttmm) REVERT: O 84 SER cc_start: 0.9294 (m) cc_final: 0.9020 (t) REVERT: O 98 ASP cc_start: 0.8942 (m-30) cc_final: 0.8019 (t0) REVERT: O 100 ASP cc_start: 0.8318 (m-30) cc_final: 0.7682 (p0) REVERT: P 5 THR cc_start: 0.7863 (m) cc_final: 0.7560 (p) REVERT: P 55 GLU cc_start: 0.8173 (tp30) cc_final: 0.7884 (tp30) REVERT: P 77 ASN cc_start: 0.8169 (t0) cc_final: 0.7849 (t0) REVERT: P 103 ARG cc_start: 0.8170 (ptt180) cc_final: 0.7892 (ttp-110) REVERT: Q 32 TYR cc_start: 0.8562 (m-10) cc_final: 0.8274 (m-10) REVERT: Q 90 TYR cc_start: 0.7671 (m-10) cc_final: 0.7464 (m-10) REVERT: R 26 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7944 (mm-40) REVERT: R 79 GLU cc_start: 0.8599 (tp30) cc_final: 0.8072 (tp30) outliers start: 41 outliers final: 26 residues processed: 333 average time/residue: 0.2054 time to fit residues: 102.8936 Evaluate side-chains 304 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 276 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain 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 A residue 123 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain M residue 132 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 O residue 89 VAL Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 92 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 50 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 280 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 291 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 208 optimal weight: 0.0980 chunk 3 optimal weight: 8.9990 chunk 249 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 268 optimal weight: 0.9980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN A 72 HIS A 425 ASN J 1 GLN ** M 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 1 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.081527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.055438 restraints weight = 63767.325| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.63 r_work: 0.2719 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 26835 Z= 0.236 Angle : 0.639 10.354 36699 Z= 0.306 Chirality : 0.046 0.331 4374 Planarity : 0.004 0.039 4440 Dihedral : 8.345 84.672 6087 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.63 % Favored : 94.27 % Rotamer: Outliers : 2.66 % Allowed : 13.95 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.15), residues: 3021 helix: -0.74 (0.27), residues: 381 sheet: -0.63 (0.17), residues: 930 loop : -1.56 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 504 TYR 0.013 0.001 TYR I 91 PHE 0.014 0.002 PHE D 87 TRP 0.023 0.001 TRP A 69 HIS 0.003 0.001 HIS M 72 Details of bonding type rmsd covalent geometry : bond 0.00551 (26655) covalent geometry : angle 0.61192 (36204) SS BOND : bond 0.00441 ( 45) SS BOND : angle 1.12027 ( 90) hydrogen bonds : bond 0.03747 ( 480) hydrogen bonds : angle 5.19864 ( 1224) link_ALPHA1-2 : bond 0.00424 ( 9) link_ALPHA1-2 : angle 1.82225 ( 27) link_ALPHA1-3 : bond 0.00957 ( 12) link_ALPHA1-3 : angle 1.55121 ( 36) link_ALPHA1-6 : bond 0.00732 ( 15) link_ALPHA1-6 : angle 1.54930 ( 45) link_BETA1-4 : bond 0.00491 ( 36) link_BETA1-4 : angle 1.78568 ( 108) link_NAG-ASN : bond 0.00355 ( 63) link_NAG-ASN : angle 1.90644 ( 189) *********************** 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 347 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 276 time to evaluate : 0.778 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: 0.7017 (m-90) cc_final: 0.6446 (m-90) REVERT: G 205 CYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7928 (m) REVERT: G 271 MET cc_start: 0.8521 (tpt) cc_final: 0.8293 (mmp) REVERT: B 626 MET cc_start: 0.8004 (ttm) cc_final: 0.7498 (mtt) REVERT: B 632 ASP cc_start: 0.9120 (t70) cc_final: 0.8671 (t0) REVERT: C 30 ARG cc_start: 0.8242 (mtt90) cc_final: 0.7851 (mtt180) REVERT: C 53 LYS cc_start: 0.9451 (ttmt) cc_final: 0.9104 (ttmm) REVERT: C 82 LYS cc_start: 0.7978 (tttp) cc_final: 0.7719 (ttmm) REVERT: C 98 ASP cc_start: 0.8964 (m-30) cc_final: 0.7880 (t0) REVERT: D 5 THR cc_start: 0.7912 (m) cc_final: 0.7515 (p) REVERT: D 77 ASN cc_start: 0.8498 (t0) cc_final: 0.8024 (t0) REVERT: D 103 ARG cc_start: 0.8077 (ptt180) cc_final: 0.7835 (ttp-110) REVERT: H 54 ARG cc_start: 0.8533 (mtt90) cc_final: 0.8070 (mmp80) REVERT: H 86 ASP cc_start: 0.8449 (t0) cc_final: 0.8051 (t0) REVERT: H 90 TYR cc_start: 0.7799 (m-10) cc_final: 0.7591 (m-10) REVERT: L 66 ASP cc_start: 0.8158 (t0) cc_final: 0.7443 (t0) REVERT: L 70 ARG cc_start: 0.7402 (mmp-170) cc_final: 0.7176 (mmp-170) REVERT: L 79 GLU cc_start: 0.8372 (tp30) cc_final: 0.7931 (tp30) REVERT: E 584 GLU cc_start: 0.8584 (mt-10) cc_final: 0.7968 (mt-10) REVERT: E 632 ASP cc_start: 0.9025 (t70) cc_final: 0.8616 (t0) REVERT: F 23 GLU cc_start: 0.7820 (mp0) cc_final: 0.7487 (mp0) REVERT: F 82 LYS cc_start: 0.7934 (tttp) cc_final: 0.7624 (ttmm) REVERT: F 98 ASP cc_start: 0.8965 (m-30) cc_final: 0.7829 (t0) REVERT: F 100 ASP cc_start: 0.8410 (m-30) cc_final: 0.7812 (p0) REVERT: I 24 GLN cc_start: 0.8128 (mt0) cc_final: 0.7777 (mp10) REVERT: I 55 GLU cc_start: 0.8507 (tp30) cc_final: 0.8237 (tp30) REVERT: I 58 VAL cc_start: 0.8541 (t) cc_final: 0.8197 (p) REVERT: I 77 ASN cc_start: 0.8782 (t0) cc_final: 0.8523 (t0) REVERT: I 103 ARG cc_start: 0.8195 (ptt180) cc_final: 0.7962 (ttp-110) REVERT: J 54 ARG cc_start: 0.8639 (mtt90) cc_final: 0.8190 (mmp80) REVERT: J 86 ASP cc_start: 0.8429 (t0) cc_final: 0.8173 (t0) REVERT: K 26 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8212 (tp-100) REVERT: K 79 GLU cc_start: 0.8501 (tp30) cc_final: 0.7981 (tp30) REVERT: K 90 MET cc_start: 0.9005 (tpp) cc_final: 0.8777 (tpp) REVERT: M 69 TRP cc_start: 0.7184 (m-90) cc_final: 0.6468 (m-90) REVERT: M 205 CYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7827 (m) REVERT: M 475 MET cc_start: 0.8546 (mmm) cc_final: 0.8070 (mmm) REVERT: N 542 ARG cc_start: 0.9176 (ttm170) cc_final: 0.8793 (ttp-170) REVERT: N 632 ASP cc_start: 0.9018 (t70) cc_final: 0.8502 (t0) REVERT: O 82 LYS cc_start: 0.7935 (tttp) cc_final: 0.7566 (ttmm) REVERT: O 84 SER cc_start: 0.9374 (m) cc_final: 0.9103 (t) REVERT: O 98 ASP cc_start: 0.8920 (m-30) cc_final: 0.7889 (t0) REVERT: P 5 THR cc_start: 0.8072 (m) cc_final: 0.7630 (p) REVERT: P 55 GLU cc_start: 0.8336 (tp30) cc_final: 0.8090 (tp30) REVERT: P 77 ASN cc_start: 0.8230 (t0) cc_final: 0.7938 (t0) REVERT: P 103 ARG cc_start: 0.8142 (ptt180) cc_final: 0.7906 (ttp-110) REVERT: Q 32 TYR cc_start: 0.8680 (m-10) cc_final: 0.8441 (m-10) REVERT: R 26 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8008 (mm-40) REVERT: R 79 GLU cc_start: 0.8585 (tp30) cc_final: 0.8086 (tp30) outliers start: 71 outliers final: 56 residues processed: 338 average time/residue: 0.1953 time to fit residues: 100.1780 Evaluate side-chains 324 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 266 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 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 24 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 242 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 21 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 75 ILE 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 8 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 430 ILE 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 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 33 VAL Chi-restraints excluded: chain R residue 92 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 180 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 272 optimal weight: 0.9990 chunk 292 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.082150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.056050 restraints weight = 63499.074| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.63 r_work: 0.2736 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26835 Z= 0.165 Angle : 0.591 10.421 36699 Z= 0.282 Chirality : 0.044 0.305 4374 Planarity : 0.004 0.042 4440 Dihedral : 8.086 83.384 6087 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.51 % Allowed : 14.70 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.15), residues: 3021 helix: -0.49 (0.27), residues: 381 sheet: -0.48 (0.17), residues: 918 loop : -1.50 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 504 TYR 0.009 0.001 TYR G 484 PHE 0.011 0.001 PHE I 87 TRP 0.026 0.001 TRP A 69 HIS 0.002 0.001 HIS C 71A Details of bonding type rmsd covalent geometry : bond 0.00388 (26655) covalent geometry : angle 0.56571 (36204) SS BOND : bond 0.00416 ( 45) SS BOND : angle 0.93083 ( 90) hydrogen bonds : bond 0.03252 ( 480) hydrogen bonds : angle 5.05091 ( 1224) link_ALPHA1-2 : bond 0.00511 ( 9) link_ALPHA1-2 : angle 1.61995 ( 27) link_ALPHA1-3 : bond 0.01026 ( 12) link_ALPHA1-3 : angle 1.51986 ( 36) link_ALPHA1-6 : bond 0.00781 ( 15) link_ALPHA1-6 : angle 1.52351 ( 45) link_BETA1-4 : bond 0.00453 ( 36) link_BETA1-4 : angle 1.63161 ( 108) link_NAG-ASN : bond 0.00260 ( 63) link_NAG-ASN : angle 1.76956 ( 189) *********************** 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 335 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 268 time to evaluate : 1.099 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: 0.7126 (m-90) cc_final: 0.6587 (m-90) REVERT: G 271 MET cc_start: 0.8544 (tpt) cc_final: 0.8273 (mmp) REVERT: B 632 ASP cc_start: 0.9111 (t70) cc_final: 0.8669 (t0) REVERT: C 5 LEU cc_start: 0.8530 (tp) cc_final: 0.8244 (tp) REVERT: C 23 GLU cc_start: 0.7627 (mp0) cc_final: 0.7376 (mp0) REVERT: C 30 ARG cc_start: 0.8232 (mtt90) cc_final: 0.7841 (mtt180) REVERT: C 53 LYS cc_start: 0.9439 (ttmt) cc_final: 0.9102 (ttmm) REVERT: C 82 LYS cc_start: 0.7947 (tttp) cc_final: 0.7683 (ttmm) REVERT: C 98 ASP cc_start: 0.8955 (m-30) cc_final: 0.7903 (t0) REVERT: D 5 THR cc_start: 0.7849 (m) cc_final: 0.7453 (p) REVERT: D 77 ASN cc_start: 0.8551 (t0) cc_final: 0.8202 (t0) REVERT: D 103 ARG cc_start: 0.8013 (ptt180) cc_final: 0.7753 (ttp-110) REVERT: H 54 ARG cc_start: 0.8601 (mtt90) cc_final: 0.8080 (mmp80) REVERT: H 86 ASP cc_start: 0.8439 (t0) cc_final: 0.8051 (t0) REVERT: H 90 TYR cc_start: 0.7792 (m-10) cc_final: 0.7546 (m-10) REVERT: H 100 MET cc_start: 0.8285 (mmt) cc_final: 0.7740 (mmt) REVERT: L 66 ASP cc_start: 0.8161 (t0) cc_final: 0.7500 (t0) REVERT: L 70 ARG cc_start: 0.7482 (mmp-170) cc_final: 0.7253 (mmp-170) REVERT: L 79 GLU cc_start: 0.8374 (tp30) cc_final: 0.7943 (tp30) REVERT: E 584 GLU cc_start: 0.8587 (mt-10) cc_final: 0.7941 (mt-10) REVERT: E 632 ASP cc_start: 0.8979 (t70) cc_final: 0.8566 (t0) REVERT: F 23 GLU cc_start: 0.7784 (mp0) cc_final: 0.7465 (mp0) REVERT: F 82 LYS cc_start: 0.7943 (tttp) cc_final: 0.7627 (ttmm) REVERT: F 98 ASP cc_start: 0.8939 (m-30) cc_final: 0.7782 (t0) REVERT: F 100 ASP cc_start: 0.8365 (m-30) cc_final: 0.7907 (p0) REVERT: I 1 ASP cc_start: 0.7815 (p0) cc_final: 0.7521 (p0) REVERT: I 5 THR cc_start: 0.8281 (m) cc_final: 0.7682 (p) REVERT: I 24 GLN cc_start: 0.8143 (mt0) cc_final: 0.7722 (mp10) REVERT: I 55 GLU cc_start: 0.8517 (tp30) cc_final: 0.8252 (tp30) REVERT: I 58 VAL cc_start: 0.8531 (t) cc_final: 0.8194 (p) REVERT: I 77 ASN cc_start: 0.8819 (t0) cc_final: 0.8573 (t0) REVERT: I 103 ARG cc_start: 0.8173 (ptt180) cc_final: 0.7927 (ttp-110) REVERT: J 54 ARG cc_start: 0.8703 (mtt90) cc_final: 0.8149 (mmp80) REVERT: J 86 ASP cc_start: 0.8413 (t0) cc_final: 0.8135 (t0) REVERT: K 70 ARG cc_start: 0.7032 (mmm160) cc_final: 0.6634 (mmp-170) REVERT: K 79 GLU cc_start: 0.8495 (tp30) cc_final: 0.7967 (tp30) REVERT: K 90 MET cc_start: 0.9031 (tpp) cc_final: 0.8768 (tpp) REVERT: M 69 TRP cc_start: 0.7128 (m-90) cc_final: 0.6425 (m-90) REVERT: M 475 MET cc_start: 0.8588 (mmm) cc_final: 0.8119 (mmm) REVERT: N 542 ARG cc_start: 0.9165 (ttm170) cc_final: 0.8748 (ttp-170) REVERT: N 621 GLU cc_start: 0.9219 (pt0) cc_final: 0.8440 (pp20) REVERT: N 632 ASP cc_start: 0.8998 (t70) cc_final: 0.8469 (t0) REVERT: O 30 ARG cc_start: 0.8280 (mtt90) cc_final: 0.7893 (mtt90) REVERT: O 82 LYS cc_start: 0.7942 (tttp) cc_final: 0.7568 (ttmm) REVERT: O 84 SER cc_start: 0.9367 (m) cc_final: 0.9089 (t) REVERT: O 98 ASP cc_start: 0.8909 (m-30) cc_final: 0.7878 (t0) REVERT: O 100 ASP cc_start: 0.8382 (m-30) cc_final: 0.7728 (p0) REVERT: P 5 THR cc_start: 0.8032 (m) cc_final: 0.7618 (p) REVERT: P 55 GLU cc_start: 0.8320 (tp30) cc_final: 0.7999 (tp30) REVERT: P 58 VAL cc_start: 0.8455 (t) cc_final: 0.8050 (p) REVERT: P 77 ASN cc_start: 0.8352 (t0) cc_final: 0.8100 (t0) REVERT: P 103 ARG cc_start: 0.8134 (ptt180) cc_final: 0.7881 (ttp-110) REVERT: Q 27 ASP cc_start: 0.6627 (t0) cc_final: 0.6258 (t0) REVERT: Q 32 TYR cc_start: 0.8682 (m-10) cc_final: 0.8423 (m-10) REVERT: Q 86 ASP cc_start: 0.8489 (t0) cc_final: 0.8281 (t0) REVERT: Q 105 LYS cc_start: 0.8924 (mmmt) cc_final: 0.8692 (mmmt) REVERT: R 70 ARG cc_start: 0.7274 (mmm160) cc_final: 0.6977 (mmp-170) REVERT: R 79 GLU cc_start: 0.8577 (tp30) cc_final: 0.8076 (tp30) outliers start: 67 outliers final: 56 residues processed: 326 average time/residue: 0.2060 time to fit residues: 101.1100 Evaluate side-chains 317 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 261 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 430 ILE Chi-restraints excluded: chain M residue 488 VAL Chi-restraints excluded: chain N residue 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 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 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 207 optimal weight: 3.9990 chunk 230 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 23 optimal weight: 0.0970 chunk 51 optimal weight: 5.9990 chunk 217 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 229 optimal weight: 0.7980 chunk 154 optimal weight: 8.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.083549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.057536 restraints weight = 62961.500| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.62 r_work: 0.2772 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26835 Z= 0.101 Angle : 0.553 11.154 36699 Z= 0.263 Chirality : 0.043 0.275 4374 Planarity : 0.003 0.039 4440 Dihedral : 7.687 81.463 6087 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.10 % Allowed : 15.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.15), residues: 3021 helix: -0.14 (0.28), residues: 381 sheet: -0.24 (0.18), residues: 906 loop : -1.37 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 504 TYR 0.009 0.001 TYR G 484 PHE 0.007 0.001 PHE G 53 TRP 0.018 0.001 TRP A 69 HIS 0.002 0.000 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00232 (26655) covalent geometry : angle 0.53107 (36204) SS BOND : bond 0.00411 ( 45) SS BOND : angle 0.80347 ( 90) hydrogen bonds : bond 0.02699 ( 480) hydrogen bonds : angle 4.86457 ( 1224) link_ALPHA1-2 : bond 0.00608 ( 9) link_ALPHA1-2 : angle 1.48541 ( 27) link_ALPHA1-3 : bond 0.01093 ( 12) link_ALPHA1-3 : angle 1.43053 ( 36) link_ALPHA1-6 : bond 0.00796 ( 15) link_ALPHA1-6 : angle 1.47993 ( 45) link_BETA1-4 : bond 0.00496 ( 36) link_BETA1-4 : angle 1.50230 ( 108) link_NAG-ASN : bond 0.00231 ( 63) link_NAG-ASN : angle 1.62412 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 277 time to evaluate : 1.064 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: 0.7014 (m-90) cc_final: 0.6595 (m-90) REVERT: G 271 MET cc_start: 0.8520 (tpt) cc_final: 0.8215 (mmp) REVERT: B 632 ASP cc_start: 0.9066 (t70) cc_final: 0.8606 (t0) REVERT: C 5 LEU cc_start: 0.8545 (tp) cc_final: 0.8175 (tp) REVERT: C 23 GLU cc_start: 0.7587 (mp0) cc_final: 0.7352 (mp0) REVERT: C 30 ARG cc_start: 0.8181 (mtt90) cc_final: 0.7725 (mtt180) REVERT: C 53 LYS cc_start: 0.9438 (ttmt) cc_final: 0.9113 (ttmm) REVERT: C 82 LYS cc_start: 0.7969 (tttp) cc_final: 0.7718 (ttmm) REVERT: C 98 ASP cc_start: 0.8946 (m-30) cc_final: 0.7904 (t0) REVERT: D 5 THR cc_start: 0.7749 (m) cc_final: 0.7454 (p) REVERT: D 60 SER cc_start: 0.8534 (t) cc_final: 0.8274 (m) REVERT: D 77 ASN cc_start: 0.8527 (t0) cc_final: 0.8245 (t0) REVERT: D 103 ARG cc_start: 0.8002 (ptt180) cc_final: 0.7738 (ttp-110) REVERT: H 54 ARG cc_start: 0.8597 (mtt90) cc_final: 0.8065 (mmp80) REVERT: H 86 ASP cc_start: 0.8471 (t0) cc_final: 0.8182 (t0) REVERT: H 90 TYR cc_start: 0.7751 (m-10) cc_final: 0.7530 (m-10) REVERT: L 66 ASP cc_start: 0.8133 (t0) cc_final: 0.7364 (t0) REVERT: L 70 ARG cc_start: 0.7506 (mmp-170) cc_final: 0.7279 (mmp-170) REVERT: L 79 GLU cc_start: 0.8391 (tp30) cc_final: 0.7955 (tp30) REVERT: A 475 MET cc_start: 0.8407 (mmm) cc_final: 0.8191 (mmt) REVERT: E 584 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8011 (mt-10) REVERT: E 632 ASP cc_start: 0.8871 (t70) cc_final: 0.8421 (t0) REVERT: F 23 GLU cc_start: 0.7762 (mp0) cc_final: 0.7426 (mp0) REVERT: F 82 LYS cc_start: 0.7942 (tttp) cc_final: 0.7641 (ttmm) REVERT: F 98 ASP cc_start: 0.8942 (m-30) cc_final: 0.7805 (t0) REVERT: F 100 ASP cc_start: 0.8272 (m-30) cc_final: 0.7902 (p0) REVERT: I 1 ASP cc_start: 0.7773 (p0) cc_final: 0.7500 (p0) REVERT: I 5 THR cc_start: 0.8199 (m) cc_final: 0.7627 (p) REVERT: I 24 GLN cc_start: 0.8134 (mt0) cc_final: 0.7720 (mp10) REVERT: I 55 GLU cc_start: 0.8516 (tp30) cc_final: 0.8253 (tp30) REVERT: I 58 VAL cc_start: 0.8489 (t) cc_final: 0.8164 (p) REVERT: I 77 ASN cc_start: 0.8826 (t0) cc_final: 0.8612 (t0) REVERT: I 103 ARG cc_start: 0.8168 (ptt180) cc_final: 0.7902 (ttp-110) REVERT: J 6 GLU cc_start: 0.7311 (pt0) cc_final: 0.7091 (pt0) REVERT: J 54 ARG cc_start: 0.8707 (mtt90) cc_final: 0.8178 (mmp80) REVERT: J 86 ASP cc_start: 0.8408 (t0) cc_final: 0.8104 (t0) REVERT: K 26 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8182 (tp-100) REVERT: K 79 GLU cc_start: 0.8494 (tp30) cc_final: 0.7972 (tp30) REVERT: K 90 MET cc_start: 0.9019 (tpp) cc_final: 0.8714 (tpp) REVERT: M 69 TRP cc_start: 0.7105 (m-90) cc_final: 0.6461 (m-90) REVERT: M 205 CYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7742 (m) REVERT: M 475 MET cc_start: 0.8567 (mmm) cc_final: 0.8075 (mmm) REVERT: M 504 ARG cc_start: 0.8378 (mmm160) cc_final: 0.8081 (mmm160) REVERT: N 542 ARG cc_start: 0.9085 (ttm170) cc_final: 0.8693 (ttp-170) REVERT: N 621 GLU cc_start: 0.9187 (pt0) cc_final: 0.8461 (pp20) REVERT: N 632 ASP cc_start: 0.8947 (t70) cc_final: 0.8411 (t0) REVERT: O 30 ARG cc_start: 0.8239 (mtt90) cc_final: 0.7978 (mtt90) REVERT: O 82 LYS cc_start: 0.7968 (tttp) cc_final: 0.7590 (ttmm) REVERT: O 84 SER cc_start: 0.9351 (m) cc_final: 0.9062 (t) REVERT: O 100 ASP cc_start: 0.8304 (m-30) cc_final: 0.7763 (p0) REVERT: P 5 THR cc_start: 0.7913 (m) cc_final: 0.7511 (p) REVERT: P 55 GLU cc_start: 0.8333 (tp30) cc_final: 0.8000 (tp30) REVERT: P 58 VAL cc_start: 0.8455 (t) cc_final: 0.8023 (p) REVERT: P 77 ASN cc_start: 0.8471 (t0) cc_final: 0.8204 (t0) REVERT: P 103 ARG cc_start: 0.8134 (ptt180) cc_final: 0.7876 (ttp-110) REVERT: Q 32 TYR cc_start: 0.8670 (m-10) cc_final: 0.8403 (m-10) REVERT: Q 86 ASP cc_start: 0.8529 (t0) cc_final: 0.8261 (t0) REVERT: Q 105 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8675 (mmmt) REVERT: R 70 ARG cc_start: 0.7228 (mmm160) cc_final: 0.6966 (mmp-170) REVERT: R 79 GLU cc_start: 0.8572 (tp30) cc_final: 0.8052 (tp30) outliers start: 56 outliers final: 41 residues processed: 326 average time/residue: 0.1972 time to fit residues: 97.2029 Evaluate side-chains 310 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 268 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 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 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 51 ILE Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 488 VAL Chi-restraints excluded: chain N residue 638 TYR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 31 ASP Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain 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 33 VAL Chi-restraints excluded: chain R residue 92 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 222 optimal weight: 0.3980 chunk 141 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 273 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 123 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 377 ASN ** M 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.084010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.058094 restraints weight = 63087.924| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.62 r_work: 0.2785 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2930 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= 0.098 Angle : 0.548 12.103 36699 Z= 0.260 Chirality : 0.043 0.272 4374 Planarity : 0.003 0.035 4440 Dihedral : 7.344 79.800 6087 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.91 % Allowed : 15.97 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.15), residues: 3021 helix: 0.13 (0.29), residues: 381 sheet: -0.04 (0.18), residues: 864 loop : -1.31 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 56 TYR 0.010 0.001 TYR J 32 PHE 0.007 0.001 PHE G 53 TRP 0.015 0.001 TRP A 69 HIS 0.002 0.000 HIS R 89 Details of bonding type rmsd covalent geometry : bond 0.00229 (26655) covalent geometry : angle 0.52690 (36204) SS BOND : bond 0.00332 ( 45) SS BOND : angle 0.79652 ( 90) hydrogen bonds : bond 0.02482 ( 480) hydrogen bonds : angle 4.66987 ( 1224) link_ALPHA1-2 : bond 0.00598 ( 9) link_ALPHA1-2 : angle 1.47313 ( 27) link_ALPHA1-3 : bond 0.01085 ( 12) link_ALPHA1-3 : angle 1.38883 ( 36) link_ALPHA1-6 : bond 0.00782 ( 15) link_ALPHA1-6 : angle 1.45674 ( 45) link_BETA1-4 : bond 0.00491 ( 36) link_BETA1-4 : angle 1.47882 ( 108) link_NAG-ASN : bond 0.00206 ( 63) link_NAG-ASN : angle 1.55697 ( 189) *********************** 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 331 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 280 time to evaluate : 1.070 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: 0.7061 (m-90) cc_final: 0.6612 (m-90) REVERT: G 271 MET cc_start: 0.8520 (tpt) cc_final: 0.8196 (mmp) REVERT: B 632 ASP cc_start: 0.9061 (t70) cc_final: 0.8613 (t0) REVERT: C 5 LEU cc_start: 0.8559 (tp) cc_final: 0.8269 (tp) REVERT: C 23 GLU cc_start: 0.7609 (mp0) cc_final: 0.7222 (mp0) REVERT: C 30 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7731 (mtt180) REVERT: C 53 LYS cc_start: 0.9458 (ttmt) cc_final: 0.9136 (ttmm) REVERT: C 82 LYS cc_start: 0.7987 (tttp) cc_final: 0.7734 (ttmm) REVERT: D 5 THR cc_start: 0.7693 (m) cc_final: 0.7389 (p) REVERT: D 60 SER cc_start: 0.8524 (t) cc_final: 0.8273 (m) REVERT: D 77 ASN cc_start: 0.8580 (t0) cc_final: 0.8315 (t0) REVERT: D 103 ARG cc_start: 0.7996 (ptt180) cc_final: 0.7736 (ttp-110) REVERT: H 86 ASP cc_start: 0.8452 (t0) cc_final: 0.8177 (t0) REVERT: H 90 TYR cc_start: 0.7786 (m-10) cc_final: 0.7529 (m-10) REVERT: L 66 ASP cc_start: 0.8157 (t0) cc_final: 0.7379 (t0) REVERT: L 79 GLU cc_start: 0.8389 (tp30) cc_final: 0.7952 (tp30) REVERT: E 632 ASP cc_start: 0.8822 (t70) cc_final: 0.8382 (t0) REVERT: F 23 GLU cc_start: 0.7763 (mp0) cc_final: 0.7416 (mp0) REVERT: F 82 LYS cc_start: 0.7943 (tttp) cc_final: 0.7657 (ttmm) REVERT: F 98 ASP cc_start: 0.8952 (m-30) cc_final: 0.7787 (t0) REVERT: F 100 ASP cc_start: 0.8297 (m-30) cc_final: 0.7763 (p0) REVERT: I 5 THR cc_start: 0.8089 (m) cc_final: 0.7535 (p) REVERT: I 24 GLN cc_start: 0.8150 (mt0) cc_final: 0.7726 (mp10) REVERT: I 55 GLU cc_start: 0.8515 (tp30) cc_final: 0.8300 (tp30) REVERT: I 58 VAL cc_start: 0.8469 (t) cc_final: 0.8119 (p) REVERT: I 103 ARG cc_start: 0.8174 (ptt180) cc_final: 0.7899 (ttp-110) REVERT: J 5 GLN cc_start: 0.9122 (tp-100) cc_final: 0.8883 (tp-100) REVERT: J 54 ARG cc_start: 0.8705 (mtt90) cc_final: 0.8165 (mmp80) REVERT: J 86 ASP cc_start: 0.8403 (t0) cc_final: 0.8099 (t0) REVERT: K 26 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8160 (tp-100) REVERT: K 66 ASP cc_start: 0.8103 (t0) cc_final: 0.7625 (t70) REVERT: K 79 GLU cc_start: 0.8501 (tp30) cc_final: 0.7977 (tp30) REVERT: K 90 MET cc_start: 0.9034 (tpp) cc_final: 0.8737 (tpp) REVERT: M 69 TRP cc_start: 0.7032 (m-90) cc_final: 0.6369 (m-90) REVERT: M 475 MET cc_start: 0.8587 (mmm) cc_final: 0.8247 (mmm) REVERT: M 504 ARG cc_start: 0.8384 (mmm160) cc_final: 0.8171 (mmm160) REVERT: N 542 ARG cc_start: 0.9099 (ttm170) cc_final: 0.8737 (ttp-170) REVERT: N 621 GLU cc_start: 0.9174 (pt0) cc_final: 0.8452 (pp20) REVERT: N 632 ASP cc_start: 0.8951 (t70) cc_final: 0.8432 (t0) REVERT: N 634 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8092 (mt-10) REVERT: O 30 ARG cc_start: 0.8263 (mtt90) cc_final: 0.7924 (mtm-85) REVERT: O 82 LYS cc_start: 0.7979 (tttp) cc_final: 0.7613 (ttmm) REVERT: O 100 ASP cc_start: 0.8295 (m-30) cc_final: 0.7774 (p0) REVERT: P 5 THR cc_start: 0.7819 (m) cc_final: 0.7481 (p) REVERT: P 55 GLU cc_start: 0.8341 (tp30) cc_final: 0.8025 (tp30) REVERT: P 58 VAL cc_start: 0.8401 (t) cc_final: 0.7967 (p) REVERT: P 77 ASN cc_start: 0.8451 (t0) cc_final: 0.8158 (t0) REVERT: P 103 ARG cc_start: 0.8144 (ptt180) cc_final: 0.7881 (ttp-110) REVERT: Q 32 TYR cc_start: 0.8672 (m-10) cc_final: 0.8378 (m-10) REVERT: Q 86 ASP cc_start: 0.8443 (t0) cc_final: 0.8173 (t0) REVERT: R 26 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7882 (mm-40) REVERT: R 79 GLU cc_start: 0.8579 (tp30) cc_final: 0.8056 (tp30) outliers start: 51 outliers final: 46 residues processed: 325 average time/residue: 0.1880 time to fit residues: 93.0532 Evaluate side-chains 316 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 270 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 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 F residue 51 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 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 132 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 425 ASN Chi-restraints excluded: chain M residue 488 VAL 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 R residue 8 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 47 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 201 optimal weight: 0.6980 chunk 164 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 127 optimal weight: 0.0270 overall best weight: 0.8840 ------------------------------------------------------------------------------- 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** M 425 ASN 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 = 0.083871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.057897 restraints weight = 63248.206| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.63 r_work: 0.2780 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26835 Z= 0.111 Angle : 0.568 12.773 36699 Z= 0.267 Chirality : 0.043 0.276 4374 Planarity : 0.003 0.053 4440 Dihedral : 7.292 79.565 6087 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.02 % Allowed : 16.31 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.15), residues: 3021 helix: 0.25 (0.29), residues: 381 sheet: -0.04 (0.18), residues: 921 loop : -1.25 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 56 TYR 0.010 0.001 TYR H 32 PHE 0.008 0.001 PHE G 53 TRP 0.012 0.001 TRP A 69 HIS 0.002 0.000 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00263 (26655) covalent geometry : angle 0.54745 (36204) SS BOND : bond 0.00326 ( 45) SS BOND : angle 0.74551 ( 90) hydrogen bonds : bond 0.02513 ( 480) hydrogen bonds : angle 4.62106 ( 1224) link_ALPHA1-2 : bond 0.00585 ( 9) link_ALPHA1-2 : angle 1.48646 ( 27) link_ALPHA1-3 : bond 0.01035 ( 12) link_ALPHA1-3 : angle 1.39313 ( 36) link_ALPHA1-6 : bond 0.00757 ( 15) link_ALPHA1-6 : angle 1.45571 ( 45) link_BETA1-4 : bond 0.00479 ( 36) link_BETA1-4 : angle 1.48236 ( 108) link_NAG-ASN : bond 0.00214 ( 63) link_NAG-ASN : angle 1.56160 ( 189) *********************** 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 328 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 274 time to evaluate : 0.975 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: 0.7071 (m-90) cc_final: 0.6613 (m-90) REVERT: G 271 MET cc_start: 0.8515 (tpt) cc_final: 0.8191 (mmp) REVERT: B 632 ASP cc_start: 0.9064 (t70) cc_final: 0.8618 (t0) REVERT: C 5 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8264 (tp) REVERT: C 23 GLU cc_start: 0.7610 (mp0) cc_final: 0.7241 (mp0) REVERT: C 30 ARG cc_start: 0.8183 (mtt90) cc_final: 0.7728 (mtt180) REVERT: C 53 LYS cc_start: 0.9441 (ttmt) cc_final: 0.9115 (ttmm) REVERT: C 82 LYS cc_start: 0.7982 (tttp) cc_final: 0.7746 (ttmm) REVERT: D 5 THR cc_start: 0.7710 (m) cc_final: 0.7405 (p) REVERT: D 58 VAL cc_start: 0.8368 (t) cc_final: 0.7926 (p) REVERT: D 60 SER cc_start: 0.8585 (t) cc_final: 0.8336 (m) REVERT: D 77 ASN cc_start: 0.8587 (t0) cc_final: 0.8326 (t0) REVERT: D 103 ARG cc_start: 0.8018 (ptt180) cc_final: 0.7753 (ttp-110) REVERT: H 86 ASP cc_start: 0.8431 (t0) cc_final: 0.8177 (t0) REVERT: H 90 TYR cc_start: 0.7732 (m-10) cc_final: 0.7487 (m-10) REVERT: L 66 ASP cc_start: 0.8174 (t0) cc_final: 0.7381 (t0) REVERT: L 70 ARG cc_start: 0.7463 (mmm160) cc_final: 0.7156 (mmm160) REVERT: L 79 GLU cc_start: 0.8406 (tp30) cc_final: 0.7971 (tp30) REVERT: A 475 MET cc_start: 0.8440 (mmm) cc_final: 0.8167 (mmt) REVERT: E 632 ASP cc_start: 0.8863 (t70) cc_final: 0.8409 (t0) REVERT: F 23 GLU cc_start: 0.7776 (mp0) cc_final: 0.7466 (mp0) REVERT: F 82 LYS cc_start: 0.7939 (tttp) cc_final: 0.7567 (ttmm) REVERT: F 98 ASP cc_start: 0.8963 (m-30) cc_final: 0.7782 (t0) REVERT: F 100 ASP cc_start: 0.8309 (m-30) cc_final: 0.7757 (p0) REVERT: I 4 MET cc_start: 0.7594 (mmt) cc_final: 0.7311 (mmm) REVERT: I 5 THR cc_start: 0.8011 (m) cc_final: 0.7480 (p) REVERT: I 24 GLN cc_start: 0.8183 (mt0) cc_final: 0.7714 (mp10) REVERT: I 55 GLU cc_start: 0.8519 (tp30) cc_final: 0.8302 (tp30) REVERT: I 58 VAL cc_start: 0.8502 (t) cc_final: 0.8173 (p) REVERT: I 103 ARG cc_start: 0.8222 (ptt180) cc_final: 0.7949 (ttp-110) REVERT: J 54 ARG cc_start: 0.8710 (mtt90) cc_final: 0.8167 (mmp80) REVERT: J 86 ASP cc_start: 0.8394 (t0) cc_final: 0.8095 (t0) REVERT: K 26 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8160 (tp-100) REVERT: K 79 GLU cc_start: 0.8502 (tp30) cc_final: 0.7978 (tp30) REVERT: K 90 MET cc_start: 0.9033 (tpp) cc_final: 0.8743 (tpp) REVERT: M 69 TRP cc_start: 0.7049 (m-90) cc_final: 0.6358 (m-90) REVERT: M 475 MET cc_start: 0.8572 (mmm) cc_final: 0.8218 (mmm) REVERT: M 504 ARG cc_start: 0.8394 (mmm160) cc_final: 0.8149 (mmm160) REVERT: N 542 ARG cc_start: 0.9096 (ttm170) cc_final: 0.8716 (ttp-170) REVERT: N 621 GLU cc_start: 0.9180 (pt0) cc_final: 0.8474 (pp20) REVERT: N 632 ASP cc_start: 0.8956 (t70) cc_final: 0.8426 (t0) REVERT: N 634 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8071 (mt-10) REVERT: O 30 ARG cc_start: 0.8294 (mtt90) cc_final: 0.7921 (mtm-85) REVERT: O 82 LYS cc_start: 0.7981 (tttp) cc_final: 0.7616 (ttmm) REVERT: O 100 ASP cc_start: 0.8319 (m-30) cc_final: 0.7751 (p0) REVERT: P 5 THR cc_start: 0.7774 (m) cc_final: 0.7463 (p) REVERT: P 55 GLU cc_start: 0.8344 (tp30) cc_final: 0.8037 (tp30) REVERT: P 58 VAL cc_start: 0.8391 (t) cc_final: 0.7961 (p) REVERT: P 77 ASN cc_start: 0.8466 (t0) cc_final: 0.8177 (t0) REVERT: P 103 ARG cc_start: 0.8143 (ptt180) cc_final: 0.7882 (ttp-110) REVERT: Q 27 ASP cc_start: 0.6475 (t0) cc_final: 0.6072 (t0) REVERT: Q 32 TYR cc_start: 0.8637 (m-10) cc_final: 0.8272 (m-10) REVERT: Q 86 ASP cc_start: 0.8440 (t0) cc_final: 0.8197 (t0) REVERT: R 26 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7943 (mm-40) REVERT: R 79 GLU cc_start: 0.8580 (tp30) cc_final: 0.8057 (tp30) outliers start: 54 outliers final: 50 residues processed: 322 average time/residue: 0.1981 time to fit residues: 96.5715 Evaluate side-chains 323 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 272 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 5 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 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 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 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 132 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 425 ASN Chi-restraints excluded: chain M residue 488 VAL 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 33 VAL Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 22 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 250 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 47 optimal weight: 0.0980 chunk 81 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** M 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.084125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.058204 restraints weight = 62858.110| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.62 r_work: 0.2789 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26835 Z= 0.103 Angle : 0.566 13.152 36699 Z= 0.267 Chirality : 0.043 0.271 4374 Planarity : 0.003 0.047 4440 Dihedral : 7.202 79.006 6087 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.06 % Allowed : 16.16 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.16), residues: 3021 helix: 0.35 (0.29), residues: 381 sheet: -0.03 (0.17), residues: 945 loop : -1.24 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 56 TYR 0.009 0.001 TYR D 91 PHE 0.007 0.001 PHE G 53 TRP 0.013 0.001 TRP A 69 HIS 0.002 0.000 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00241 (26655) covalent geometry : angle 0.54641 (36204) SS BOND : bond 0.00324 ( 45) SS BOND : angle 0.71614 ( 90) hydrogen bonds : bond 0.02465 ( 480) hydrogen bonds : angle 4.57241 ( 1224) link_ALPHA1-2 : bond 0.00602 ( 9) link_ALPHA1-2 : angle 1.47743 ( 27) link_ALPHA1-3 : bond 0.01029 ( 12) link_ALPHA1-3 : angle 1.39081 ( 36) link_ALPHA1-6 : bond 0.00755 ( 15) link_ALPHA1-6 : angle 1.44253 ( 45) link_BETA1-4 : bond 0.00483 ( 36) link_BETA1-4 : angle 1.45762 ( 108) link_NAG-ASN : bond 0.00213 ( 63) link_NAG-ASN : angle 1.53757 ( 189) ********************** 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 333 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 278 time to evaluate : 1.010 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: 0.7069 (m-90) cc_final: 0.6630 (m-90) REVERT: B 632 ASP cc_start: 0.9055 (t70) cc_final: 0.8609 (t0) REVERT: C 5 LEU cc_start: 0.8549 (tp) cc_final: 0.8267 (tp) REVERT: C 23 GLU cc_start: 0.7608 (mp0) cc_final: 0.7232 (mp0) REVERT: C 30 ARG cc_start: 0.8173 (mtt90) cc_final: 0.7721 (mtt180) REVERT: C 53 LYS cc_start: 0.9440 (ttmt) cc_final: 0.9115 (ttmm) REVERT: C 82 LYS cc_start: 0.7976 (tttp) cc_final: 0.7733 (ttmm) REVERT: D 5 THR cc_start: 0.7713 (m) cc_final: 0.7410 (p) REVERT: D 58 VAL cc_start: 0.8429 (t) cc_final: 0.7994 (p) REVERT: D 60 SER cc_start: 0.8567 (t) cc_final: 0.8328 (m) REVERT: D 77 ASN cc_start: 0.8577 (t0) cc_final: 0.8316 (t0) REVERT: D 103 ARG cc_start: 0.8022 (ptt180) cc_final: 0.7761 (ttp-110) REVERT: H 86 ASP cc_start: 0.8427 (t0) cc_final: 0.8178 (t0) REVERT: H 90 TYR cc_start: 0.7711 (m-10) cc_final: 0.7485 (m-10) REVERT: L 66 ASP cc_start: 0.8162 (t0) cc_final: 0.7954 (t0) REVERT: L 79 GLU cc_start: 0.8405 (tp30) cc_final: 0.7968 (tp30) REVERT: A 114 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8831 (mm-40) REVERT: A 475 MET cc_start: 0.8434 (mmm) cc_final: 0.8196 (mmt) REVERT: A 502 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8230 (tptp) REVERT: E 632 ASP cc_start: 0.8848 (t70) cc_final: 0.8421 (t0) REVERT: F 23 GLU cc_start: 0.7768 (mp0) cc_final: 0.7460 (mp0) REVERT: F 82 LYS cc_start: 0.7938 (tttp) cc_final: 0.7572 (ttmm) REVERT: F 84 SER cc_start: 0.9372 (t) cc_final: 0.9141 (m) REVERT: F 98 ASP cc_start: 0.8958 (m-30) cc_final: 0.7770 (t0) REVERT: F 100 ASP cc_start: 0.8289 (m-30) cc_final: 0.7751 (p0) REVERT: I 4 MET cc_start: 0.7496 (mmt) cc_final: 0.7285 (mmm) REVERT: I 5 THR cc_start: 0.7973 (m) cc_final: 0.7457 (p) REVERT: I 24 GLN cc_start: 0.8193 (mt0) cc_final: 0.7716 (mp10) REVERT: I 55 GLU cc_start: 0.8504 (tp30) cc_final: 0.8284 (tp30) REVERT: I 58 VAL cc_start: 0.8442 (t) cc_final: 0.8111 (p) REVERT: I 103 ARG cc_start: 0.8223 (ptt180) cc_final: 0.7949 (ttp-110) REVERT: J 54 ARG cc_start: 0.8735 (mtt90) cc_final: 0.8151 (mmp80) REVERT: J 86 ASP cc_start: 0.8409 (t0) cc_final: 0.8131 (t0) REVERT: K 26 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8133 (tp-100) REVERT: K 79 GLU cc_start: 0.8500 (tp30) cc_final: 0.7975 (tp30) REVERT: K 90 MET cc_start: 0.9034 (tpp) cc_final: 0.8740 (tpp) REVERT: M 69 TRP cc_start: 0.7029 (m-90) cc_final: 0.6349 (m-90) REVERT: M 475 MET cc_start: 0.8567 (mmm) cc_final: 0.8205 (mmm) REVERT: M 504 ARG cc_start: 0.8415 (mmm160) cc_final: 0.8179 (mmm160) REVERT: N 542 ARG cc_start: 0.9093 (ttm170) cc_final: 0.8718 (ttp-170) REVERT: N 621 GLU cc_start: 0.9159 (pt0) cc_final: 0.8509 (pp20) REVERT: N 632 ASP cc_start: 0.8951 (t70) cc_final: 0.8420 (t0) REVERT: N 634 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8072 (mt-10) REVERT: O 30 ARG cc_start: 0.8282 (mtt90) cc_final: 0.7921 (mtm-85) REVERT: O 82 LYS cc_start: 0.7976 (tttp) cc_final: 0.7616 (ttmm) REVERT: O 100 ASP cc_start: 0.8301 (m-30) cc_final: 0.7753 (p0) REVERT: P 5 THR cc_start: 0.7750 (m) cc_final: 0.7453 (p) REVERT: P 55 GLU cc_start: 0.8341 (tp30) cc_final: 0.8035 (tp30) REVERT: P 58 VAL cc_start: 0.8372 (t) cc_final: 0.7948 (p) REVERT: P 77 ASN cc_start: 0.8424 (t0) cc_final: 0.8135 (t0) REVERT: P 103 ARG cc_start: 0.8172 (ptt180) cc_final: 0.7913 (ttp-110) REVERT: Q 27 ASP cc_start: 0.6404 (t0) cc_final: 0.5923 (t0) REVERT: Q 32 TYR cc_start: 0.8639 (m-10) cc_final: 0.8246 (m-10) REVERT: Q 86 ASP cc_start: 0.8359 (t0) cc_final: 0.8123 (t0) REVERT: R 26 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7893 (mm-40) REVERT: R 79 GLU cc_start: 0.8575 (tp30) cc_final: 0.8053 (tp30) outliers start: 55 outliers final: 49 residues processed: 329 average time/residue: 0.1934 time to fit residues: 96.2099 Evaluate side-chains 325 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 275 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain C residue 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 8 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 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 A residue 502 LYS Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain 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 132 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 488 VAL Chi-restraints excluded: chain 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 33 VAL Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 169 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 266 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 274 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN M 103 GLN ** M 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.081876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.055940 restraints weight = 63690.184| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.63 r_work: 0.2734 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3159 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= 0.196 Angle : 0.624 12.808 36699 Z= 0.296 Chirality : 0.044 0.313 4374 Planarity : 0.004 0.056 4440 Dihedral : 7.526 80.913 6087 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 2.14 % Allowed : 16.35 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.15), residues: 3021 helix: 0.26 (0.29), residues: 381 sheet: -0.20 (0.17), residues: 972 loop : -1.31 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 56 TYR 0.012 0.001 TYR D 91 PHE 0.012 0.001 PHE I 87 TRP 0.021 0.001 TRP A 69 HIS 0.002 0.001 HIS G 72 Details of bonding type rmsd covalent geometry : bond 0.00464 (26655) covalent geometry : angle 0.60192 (36204) SS BOND : bond 0.00388 ( 45) SS BOND : angle 0.97307 ( 90) hydrogen bonds : bond 0.03163 ( 480) hydrogen bonds : angle 4.68824 ( 1224) link_ALPHA1-2 : bond 0.00465 ( 9) link_ALPHA1-2 : angle 1.64899 ( 27) link_ALPHA1-3 : bond 0.00930 ( 12) link_ALPHA1-3 : angle 1.42854 ( 36) link_ALPHA1-6 : bond 0.00699 ( 15) link_ALPHA1-6 : angle 1.40699 ( 45) link_BETA1-4 : bond 0.00431 ( 36) link_BETA1-4 : angle 1.61454 ( 108) link_NAG-ASN : bond 0.00294 ( 63) link_NAG-ASN : angle 1.71944 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5794.15 seconds wall clock time: 100 minutes 21.69 seconds (6021.69 seconds total)