Starting phenix.real_space_refine on Sun Sep 13 18:17:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nb7_0404/09_2026/6nb7_0404.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nb7_0404/09_2026/6nb7_0404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6nb7_0404/09_2026/6nb7_0404.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nb7_0404/09_2026/6nb7_0404.cif" model { file = "/net/cci-nas-00/data/ceres_data/6nb7_0404/09_2026/6nb7_0404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nb7_0404/09_2026/6nb7_0404.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nb7_0404/09_2026/6nb7_0404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nb7_0404/09_2026/6nb7_0404.map" } resolution = 4.5 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= 0.010 sd= 0.129 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 127 5.16 5 C 15294 2.51 5 N 4327 2.21 5 O 4970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.14s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24718 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 6609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 6609 Classifications: {'peptide': 1049} Incomplete info: {'truncation_to_alanine': 474} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 995} Chain breaks: 7 Unresolved non-hydrogen bonds: 1662 Unresolved non-hydrogen angles: 2149 Unresolved non-hydrogen dihedrals: 1348 Unresolved non-hydrogen chiralities: 172 Planarities with less than four sites: {'ARG:plan': 18, 'GLN:plan1': 20, 'HIS:plan': 6, 'ASP:plan': 50, 'GLU:plan': 29, 'PHE:plan': 35, 'ASN:plan1': 33, 'TRP:plan': 4, 'TYR:plan': 21} Unresolved non-hydrogen planarities: 958 Chain: "B" Number of atoms: 6428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 6428 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 491} Link IDs: {'PCIS': 2, 'PTRANS': 50, 'TRANS': 979} Chain breaks: 9 Unresolved non-hydrogen bonds: 1726 Unresolved non-hydrogen angles: 2237 Unresolved non-hydrogen dihedrals: 1401 Unresolved non-hydrogen chiralities: 176 Planarities with less than four sites: {'ARG:plan': 21, 'TYR:plan': 26, 'GLN:plan1': 22, 'HIS:plan': 6, 'ASP:plan': 51, 'GLU:plan': 26, 'PHE:plan': 34, 'ASN:plan1': 37, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 1013 Chain: "C" Number of atoms: 6394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 6394 Classifications: {'peptide': 1048} Incomplete info: {'truncation_to_alanine': 561} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 994} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1865 Unresolved non-hydrogen angles: 2410 Unresolved non-hydrogen dihedrals: 1481 Unresolved non-hydrogen chiralities: 218 Planarities with less than four sites: {'ARG:plan': 21, 'TYR:plan': 21, 'GLN:plan1': 30, 'HIS:plan': 8, 'ASP:plan': 51, 'GLU:plan': 30, 'PHE:plan': 30, 'ASN:plan1': 40, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 1012 Chain: "D" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 613 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 388 Unresolved non-hydrogen angles: 504 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 3, 'ARG:plan': 10, 'PHE:plan': 6, 'ASN:plan1': 4, 'TYR:plan': 7, 'HIS:plan': 3, 'TRP:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 256 Chain: "E" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 557 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 7, 'TYR:plan': 5, 'ASP:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 189 Chain: "G" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 613 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 388 Unresolved non-hydrogen angles: 504 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 3, 'ARG:plan': 10, 'PHE:plan': 6, 'ASN:plan1': 4, 'TYR:plan': 7, 'HIS:plan': 3, 'TRP:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 256 Chain: "H" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 613 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 388 Unresolved non-hydrogen angles: 504 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 3, 'ARG:plan': 10, 'PHE:plan': 6, 'ASN:plan1': 4, 'TYR:plan': 7, 'HIS:plan': 3, 'TRP:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 256 Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 557 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 7, 'TYR:plan': 5, 'ASP:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 189 Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 557 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 7, 'TYR:plan': 5, 'ASP:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 189 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" 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 chiralities: 5 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" 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 chiralities: 5 Chain: "S" 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 chiralities: 5 Chain: "T" 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 chiralities: 4 Chain: "U" 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 chiralities: 5 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" 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 chiralities: 5 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 4 Chain: "g" 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 chiralities: 4 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "s" 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 chiralities: 4 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.77, per 1000 atoms: 0.23 Number of scatterers: 24718 At special positions: 0 Unit cell: (140.288, 163.085, 226.214, 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 127 16.00 O 4970 8.00 N 4327 7.00 C 15294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.01 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.06 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.11 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.02 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.10 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.04 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.09 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.02 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.05 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.02 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.10 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.06 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.06 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.05 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.02 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.04 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.02 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.06 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.07 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.06 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 93 " distance=2.08 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.08 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 ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " " BMA d 3 " - " MAN d 4 " " BMA q 3 " - " MAN q 4 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA P 3 " - " MAN P 5 " " BMA R 3 " - " MAN R 5 " " BMA S 3 " - " MAN S 5 " " BMA U 3 " - " MAN U 5 " " BMA d 3 " - " MAN d 5 " " BMA f 3 " - " MAN f 4 " " BMA g 3 " - " MAN g 4 " " BMA q 3 " - " MAN q 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 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 O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " 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 g 2 " - " BMA g 3 " " 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 j 2 " - " BMA j 3 " " 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 q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " NAG-ASN " NAG A1301 " - " ASN A 357 " " NAG A1302 " - " ASN A 65 " " NAG A1303 " - " ASN A 73 " " NAG A1310 " - " ASN A 158 " " NAG A1311 " - " ASN A 227 " " NAG A1321 " - " ASN A 589 " " NAG B1301 " - " ASN B 357 " " NAG B1302 " - " ASN B 29 " " NAG B1303 " - " ASN B 65 " " NAG B1309 " - " ASN B 158 " " NAG B1310 " - " ASN B 227 " " NAG B1320 " - " ASN B 589 " " NAG C1301 " - " ASN C 357 " " NAG C1302 " - " ASN C 65 " " NAG C1303 " - " ASN C 73 " " NAG C1320 " - " ASN C 589 " " NAG F 1 " - " ASN A 109 " " NAG J 1 " - " ASN A 119 " " NAG K 1 " - " ASN A 269 " " NAG M 1 " - " ASN A 318 " " NAG N 1 " - " ASN A 330 " " NAG O 1 " - " ASN A 602 " " NAG P 1 " - " ASN A 691 " " NAG Q 1 " - " ASN A 699 " " NAG R 1 " - " ASN A 783 " " NAG S 1 " - " ASN A1056 " " NAG T 1 " - " ASN A1080 " " NAG U 1 " - " ASN A1116 " " NAG V 1 " - " ASN B 109 " " NAG W 1 " - " ASN B 119 " " NAG X 1 " - " ASN B 269 " " NAG Y 1 " - " ASN B 318 " " NAG Z 1 " - " ASN B 330 " " NAG a 1 " - " ASN B 602 " " NAG b 1 " - " ASN B 691 " " NAG c 1 " - " ASN B 699 " " NAG d 1 " - " ASN B 783 " " NAG e 1 " - " ASN B1056 " " NAG f 1 " - " ASN B1080 " " NAG g 1 " - " ASN B1116 " " NAG h 1 " - " ASN C 109 " " NAG i 1 " - " ASN C 119 " " NAG j 1 " - " ASN C 227 " " NAG k 1 " - " ASN C 269 " " NAG l 1 " - " ASN C 318 " " NAG m 1 " - " ASN C 330 " " NAG n 1 " - " ASN C 602 " " NAG o 1 " - " ASN C 691 " " NAG p 1 " - " ASN C 699 " " NAG q 1 " - " ASN C 783 " " NAG r 1 " - " ASN C1056 " " NAG s 1 " - " ASN C1080 " " NAG t 1 " - " ASN C1116 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.2 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7150 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 66 sheets defined 22.1% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.601A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 removed outlier: 4.345A pdb=" N ARG A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 395' Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 602 through 612 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.627A pdb=" N ILE A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 755 " --> pdb=" O GLY A 751 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 756 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 806 Processing helix chain 'A' and resid 848 through 867 removed outlier: 3.929A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.014A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 Processing helix chain 'A' and resid 927 through 947 Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 959 through 964 Processing helix chain 'A' and resid 967 through 1015 Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1122 through 1127 Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 370 through 377 removed outlier: 4.680A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 removed outlier: 4.246A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 602 through 612 Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 728 through 737 Processing helix chain 'B' and resid 740 through 765 removed outlier: 3.597A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL B 763 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 805 Processing helix chain 'B' and resid 848 through 866 Processing helix chain 'B' and resid 867 through 870 removed outlier: 3.841A pdb=" N PHE B 870 " --> pdb=" O GLY B 867 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 867 through 870' Processing helix chain 'B' and resid 879 through 892 Processing helix chain 'B' and resid 895 through 901 removed outlier: 3.920A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.507A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 959 through 964 Processing helix chain 'B' and resid 967 through 1015 Processing helix chain 'B' and resid 1098 through 1100 No H-bonds generated for 'chain 'B' and resid 1098 through 1100' Processing helix chain 'B' and resid 1122 through 1127 Processing helix chain 'C' and resid 281 through 290 Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 370 through 377 removed outlier: 3.832A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASN C 375 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 397 removed outlier: 3.951A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 602 through 612 Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 731 through 736 removed outlier: 3.663A pdb=" N LEU C 735 " --> pdb=" O CYS C 731 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 731 through 736' Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 740 through 765 Processing helix chain 'C' and resid 798 through 806 Processing helix chain 'C' and resid 848 through 867 removed outlier: 3.742A pdb=" N THR C 865 " --> pdb=" O SER C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 870 No H-bonds generated for 'chain 'C' and resid 868 through 870' Processing helix chain 'C' and resid 879 through 892 Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.095A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 922 Processing helix chain 'C' and resid 927 through 947 Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 959 through 966 removed outlier: 3.759A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG C 965 " --> pdb=" O ASP C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 1015 removed outlier: 3.668A pdb=" N GLU C 972 " --> pdb=" O PRO C 968 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL C 973 " --> pdb=" O PRO C 969 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 108 through 112 Processing helix chain 'E' and resid 84 through 88 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 108 through 112 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 108 through 112 Processing helix chain 'I' and resid 84 through 88 Processing helix chain 'L' and resid 84 through 88 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 8.269A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N PHE A 213 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ARG A 38 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N LEU A 216 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.695A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 59 removed outlier: 7.597A pdb=" N THR A 261 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ASP A 277 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N MET A 263 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA A 275 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS A 265 " --> pdb=" O THR A 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.511A pdb=" N PHE A 161 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 131 through 138 removed outlier: 6.852A pdb=" N GLU A 131 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE A 152 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N ASN A 135 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N THR A 150 " --> pdb=" O ASN A 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 615 through 616 removed outlier: 5.364A pdb=" N ILE A 299 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N THR A 585 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLN A 301 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A 583 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 303 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 314 removed outlier: 5.802A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE A 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 341 through 345 Processing sheet with id=AB1, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.532A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AB3, first strand: chain 'A' and resid 640 through 646 removed outlier: 5.263A pdb=" N THR A 678 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR A 644 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 683 through 684 removed outlier: 6.016A pdb=" N ALA A 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 693 through 697 Processing sheet with id=AB6, first strand: chain 'A' and resid 700 through 710 removed outlier: 3.619A pdb=" N ALA A1038 " --> pdb=" O GLY A1041 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.200A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 769 through 771 removed outlier: 6.273A pdb=" N MET A 770 " --> pdb=" O SER B 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AC1, first strand: chain 'A' and resid 1102 through 1107 removed outlier: 4.835A pdb=" N ALA A1069 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 31 through 34 removed outlier: 3.546A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 31 through 34 removed outlier: 3.546A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 46 through 47 removed outlier: 6.599A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 51 through 59 removed outlier: 7.654A pdb=" N THR B 261 " --> pdb=" O ASP B 277 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ASP B 277 " --> pdb=" O THR B 261 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET B 263 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA B 275 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS B 265 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 80 through 82 removed outlier: 6.114A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 123 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR B 163 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE B 125 " --> pdb=" O PHE B 161 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE B 161 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ALA B 127 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N CYS B 159 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN B 155 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N CYS B 133 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE B 153 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN B 135 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N MET B 151 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 615 through 616 removed outlier: 5.246A pdb=" N ILE B 299 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR B 585 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 303 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 341 through 345 removed outlier: 6.313A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 341 through 345 removed outlier: 6.987A pdb=" N GLU B 502 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL B 382 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N SER B 500 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA B 384 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL B 498 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER B 386 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B 496 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL B 388 " --> pdb=" O TYR B 494 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR B 494 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N PHE B 501 " --> pdb=" O MET B 417 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N MET B 417 " --> pdb=" O PHE B 501 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLY B 418 " --> pdb=" O TYR B 367 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AD2, first strand: chain 'B' and resid 640 through 646 removed outlier: 6.308A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N VAL B 642 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 693 through 697 removed outlier: 3.935A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B1083 " --> pdb=" O ASN B1080 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLN B1088 " --> pdb=" O SER B1093 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER B1093 " --> pdb=" O GLN B1088 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 700 through 710 removed outlier: 3.578A pdb=" N ALA B1038 " --> pdb=" O GLY B1041 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.353A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 769 through 771 Processing sheet with id=AD7, first strand: chain 'B' and resid 1102 through 1107 removed outlier: 4.972A pdb=" N ALA B1069 " --> pdb=" O SER B1105 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.939A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 51 through 59 removed outlier: 7.700A pdb=" N THR C 261 " --> pdb=" O ASP C 277 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASP C 277 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N MET C 263 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA C 275 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LYS C 265 " --> pdb=" O THR C 273 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AE2, first strand: chain 'C' and resid 132 through 137 removed outlier: 7.211A pdb=" N ILE C 152 " --> pdb=" O CYS C 133 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 615 through 616 removed outlier: 5.271A pdb=" N ILE C 299 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR C 585 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN C 301 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C 583 " --> pdb=" O GLN C 301 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER C 303 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.638A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS C 419 " --> pdb=" O LEU C 499 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.847A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE7, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.659A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 693 through 697 Processing sheet with id=AE9, first strand: chain 'C' and resid 700 through 710 removed outlier: 3.668A pdb=" N ALA C1038 " --> pdb=" O GLY C1041 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.357A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AF3, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 4.744A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.718A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.718A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.048A pdb=" N GLN E 42 " --> pdb=" O ARG E 51 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG E 51 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 14 Processing sheet with id=AG1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.693A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.693A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG5, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.647A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.647A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'I' and resid 10 through 14 removed outlier: 6.031A pdb=" N GLN I 42 " --> pdb=" O ARG I 51 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ARG I 51 " --> pdb=" O GLN I 42 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 10 through 14 Processing sheet with id=AH1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AH2, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.023A pdb=" N GLN L 42 " --> pdb=" O ARG L 51 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ARG L 51 " --> pdb=" O GLN L 42 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 10 through 14 1352 hydrogen bonds defined for protein. 3576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.40 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7524 1.33 - 1.46: 6778 1.46 - 1.59: 10655 1.59 - 1.73: 2 1.73 - 1.86: 152 Bond restraints: 25111 Sorted by residual: bond pdb=" C1 NAG Z 1 " pdb=" O5 NAG Z 1 " ideal model delta sigma weight residual 1.406 1.555 -0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.553 -0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.551 -0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.550 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.15e+01 ... (remaining 25106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 33657 3.96 - 7.92: 954 7.92 - 11.88: 11 11.88 - 15.84: 0 15.84 - 19.79: 2 Bond angle restraints: 34624 Sorted by residual: angle pdb=" N PHE B 784 " pdb=" CA PHE B 784 " pdb=" CB PHE B 784 " ideal model delta sigma weight residual 111.20 95.17 16.03 1.65e+00 3.67e-01 9.44e+01 angle pdb=" CG1 VAL B 808 " pdb=" CB VAL B 808 " pdb=" CG2 VAL B 808 " ideal model delta sigma weight residual 110.80 130.59 -19.79 2.20e+00 2.07e-01 8.10e+01 angle pdb=" N PHE B 784 " pdb=" CA PHE B 784 " pdb=" C PHE B 784 " ideal model delta sigma weight residual 112.41 100.76 11.65 1.30e+00 5.92e-01 8.03e+01 angle pdb=" C THR C 468 " pdb=" N PRO C 469 " pdb=" CA PRO C 469 " ideal model delta sigma weight residual 119.66 126.00 -6.34 7.30e-01 1.88e+00 7.55e+01 angle pdb=" C THR A 468 " pdb=" N PRO A 469 " pdb=" CA PRO A 469 " ideal model delta sigma weight residual 119.66 125.62 -5.96 7.20e-01 1.93e+00 6.85e+01 ... (remaining 34619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 13500 17.84 - 35.68: 234 35.68 - 53.52: 60 53.52 - 71.36: 28 71.36 - 89.20: 10 Dihedral angle restraints: 13832 sinusoidal: 2810 harmonic: 11022 Sorted by residual: dihedral pdb=" N PHE B 784 " pdb=" C PHE B 784 " pdb=" CA PHE B 784 " pdb=" CB PHE B 784 " ideal model delta harmonic sigma weight residual 122.80 98.71 24.09 0 2.50e+00 1.60e-01 9.29e+01 dihedral pdb=" CB CYS A 524 " pdb=" SG CYS A 524 " pdb=" SG CYS A 576 " pdb=" CB CYS A 576 " ideal model delta sinusoidal sigma weight residual -86.00 -147.06 61.06 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS C 524 " pdb=" SG CYS C 524 " pdb=" SG CYS C 576 " pdb=" CB CYS C 576 " ideal model delta sinusoidal sigma weight residual -86.00 -143.91 57.91 1 1.00e+01 1.00e-02 4.50e+01 ... (remaining 13829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 4243 0.152 - 0.304: 302 0.304 - 0.456: 31 0.456 - 0.608: 31 0.608 - 0.760: 1 Chirality restraints: 4608 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.73 0.33 2.00e-02 2.50e+03 2.78e+02 chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.73 0.33 2.00e-02 2.50e+03 2.77e+02 chirality pdb=" C1 NAG h 2 " pdb=" O4 NAG h 1 " pdb=" C2 NAG h 2 " pdb=" O5 NAG h 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.72 0.32 2.00e-02 2.50e+03 2.53e+02 ... (remaining 4605 not shown) Planarity restraints: 4606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 357 " -0.029 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" CG ASN C 357 " 0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN C 357 " -0.215 2.00e-02 2.50e+03 pdb=" ND2 ASN C 357 " 0.514 2.00e-02 2.50e+03 pdb=" C1 NAG C1301 " -0.339 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 783 " -0.081 2.00e-02 2.50e+03 1.02e-01 1.31e+02 pdb=" CG ASN B 783 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 783 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 783 " 0.174 2.00e-02 2.50e+03 pdb=" C1 NAG d 1 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 269 " -0.073 2.00e-02 2.50e+03 7.83e-02 7.66e+01 pdb=" CG ASN C 269 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN C 269 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 269 " 0.121 2.00e-02 2.50e+03 pdb=" C1 NAG k 1 " -0.095 2.00e-02 2.50e+03 ... (remaining 4603 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 8962 2.84 - 3.36: 20867 3.36 - 3.87: 36536 3.87 - 4.39: 37481 4.39 - 4.90: 65257 Nonbonded interactions: 169103 Sorted by model distance: nonbonded pdb=" N ASN A 109 " pdb=" OD1 ASN A 109 " model vdw 2.330 3.120 nonbonded pdb=" N ASN A 691 " pdb=" OD1 ASN A 691 " model vdw 2.356 3.120 nonbonded pdb=" N ASN C 691 " pdb=" OD1 ASN C 691 " model vdw 2.389 3.120 nonbonded pdb=" O3 NAG l 1 " pdb=" O5 NAG l 2 " model vdw 2.394 3.040 nonbonded pdb=" N ASN C 109 " pdb=" OD1 ASN C 109 " model vdw 2.397 3.120 ... (remaining 169098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 36 or (resid 37 through 38 and (name N or name \ CA or name C or name O or name CB )) or resid 39 through 58 or (resid 59 through \ 60 and (name N or name CA or name C or name O or name CB )) or resid 61 through \ 72 or (resid 73 through 78 and (name N or name CA or name C or name O or name C \ B )) or resid 79 through 87 or (resid 88 through 99 and (name N or name CA or na \ me C or name O or name CB )) or resid 100 through 137 or (resid 149 through 158 \ and (name N or name CA or name C or name O or name CB )) or resid 159 through 16 \ 8 or (resid 179 through 198 and (name N or name CA or name C or name O or name C \ B )) or resid 199 through 237 or (resid 251 through 265 and (name N or name CA o \ r name C or name O or name CB )) or resid 266 through 279 or (resid 280 through \ 281 and (name N or name CA or name C or name O or name CB )) or resid 282 throug \ h 284 or (resid 285 through 286 and (name N or name CA or name C or name O or na \ me CB )) or resid 287 through 289 or (resid 290 through 291 and (name N or name \ CA or name C or name O or name CB )) or resid 292 through 301 or (resid 302 thro \ ugh 303 and (name N or name CA or name C or name O or name CB )) or resid 304 th \ rough 306 or (resid 307 through 308 and (name N or name CA or name C or name O o \ r name CB )) or resid 309 through 312 or (resid 313 through 316 and (name N or n \ ame CA or name C or name O or name CB )) or resid 317 through 483 or resid 492 t \ hrough 502 or resid 509 through 529 or (resid 530 and (name N or name CA or name \ C or name O or name CB )) or resid 531 or (resid 532 through 533 and (name N or \ name CA or name C or name O or name CB )) or resid 534 through 542 or (resid 54 \ 3 through 544 and (name N or name CA or name C or name O or name CB )) or resid \ 545 through 557 or (resid 558 through 564 and (name N or name CA or name C or na \ me O or name CB )) or resid 565 through 569 or (resid 570 through 574 and (name \ N or name CA or name C or name O or name CB )) or resid 575 through 580 or (resi \ d 581 through 585 and (name N or name CA or name C or name O or name CB )) or re \ sid 586 through 587 or (resid 588 and (name N or name CA or name C or name O or \ name CB )) or resid 589 through 590 or (resid 591 through 597 and (name N or nam \ e CA or name C or name O or name CB )) or resid 598 through 600 or (resid 601 an \ d (name N or name CA or name C or name O or name CB )) or resid 602 through 603 \ or (resid 604 through 616 and (name N or name CA or name C or name O or name CB \ )) or resid 617 through 620 or (resid 621 through 624 and (name N or name CA or \ name C or name O or name CB )) or (resid 625 through 628 and (name N or name CA \ or name C or name O or name CB )) or resid 629 through 630 or (resid 631 through \ 633 and (name N or name CA or name C or name O or name CB )) or resid 634 throu \ gh 640 or (resid 641 through 645 and (name N or name CA or name C or name O or n \ ame CB )) or resid 646 through 648 or (resid 649 through 650 and (name N or name \ CA or name C or name O or name CB )) or resid 651 or (resid 652 and (name N or \ name CA or name C or name O or name CB )) or (resid 653 through 656 and (name N \ or name CA or name C or name O or name CB )) or resid 657 through 663 or (resid \ 671 through 676 and (name N or name CA or name C or name O or name CB )) or resi \ d 677 through 679 or (resid 680 and (name N or name CA or name C or name O or na \ me CB )) or resid 681 through 683 or (resid 684 through 690 and (name N or name \ CA or name C or name O or name CB )) or resid 691 through 714 or (resid 715 thro \ ugh 716 and (name N or name CA or name C or name O or name CB )) or resid 717 or \ (resid 718 through 719 and (name N or name CA or name C or name O or name CB )) \ or resid 720 through 723 or (resid 724 and (name N or name CA or name C or name \ O or name CB )) or resid 725 through 727 or (resid 728 through 730 and (name N \ or name CA or name C or name O or name CB )) or resid 731 through 733 or (resid \ 734 through 737 and (name N or name CA or name C or name O or name CB )) or resi \ d 738 through 743 or (resid 744 and (name N or name CA or name C or name O or na \ me CB )) or resid 745 through 768 or (resid 769 through 770 and (name N or name \ CA or name C or name O or name CB )) or resid 771 through 776 or (resid 777 and \ (name N or name CA or name C or name O or name CB )) or resid 778 through 786 or \ (resid 787 through 788 and (name N or name CA or name C or name O or name CB )) \ or resid 789 through 791 or (resid 792 through 793 and (name N or name CA or na \ me C or name O or name CB )) or resid 794 or (resid 795 through 796 and (name N \ or name CA or name C or name O or name CB )) or resid 797 or (resid 798 and (nam \ e N or name CA or name C or name O or name CB )) or resid 799 or (resid 800 thro \ ugh 802 and (name N or name CA or name C or name O or name CB )) or resid 803 or \ (resid 804 and (name N or name CA or name C or name O or name CB )) or resid 80 \ 5 through 808 or (resid 819 and (name N or name CA or name C or name O or name C \ B )) or resid 820 through 837 or (resid 838 and (name N or name CA or name C or \ name O or name CB )) or resid 839 or (resid 840 through 843 and (name N or name \ CA or name C or name O or name CB )) or resid 844 through 845 or (resid 846 and \ (name N or name CA or name C or name O or name CB )) or resid 847 through 849 or \ (resid 850 and (name N or name CA or name C or name O or name CB )) or resid 85 \ 1 through 864 or (resid 865 through 866 and (name N or name CA or name C or name \ O or name CB )) or resid 867 through 875 or (resid 876 through 877 and (name N \ or name CA or name C or name O or name CB )) or resid 878 through 881 or (resid \ 882 through 885 and (name N or name CA or name C or name O or name CB )) or resi \ d 886 through 892 or (resid 893 through 895 and (name N or name CA or name C or \ name O or name CB )) or resid 896 through 902 or (resid 903 through 904 and (nam \ e N or name CA or name C or name O or name CB )) or resid 905 through 913 or (re \ sid 914 through 915 and (name N or name CA or name C or name O or name CB )) or \ resid 916 or (resid 917 through 919 and (name N or name CA or name C or name O o \ r name CB )) or resid 920 or (resid 921 through 927 and (name N or name CA or na \ me C or name O or name CB )) or resid 928 through 930 or (resid 931 through 932 \ and (name N or name CA or name C or name O or name CB )) or resid 933 through 93 \ 5 or (resid 936 through 940 and (name N or name CA or name C or name O or name C \ B )) or resid 941 through 943 or (resid 944 and (name N or name CA or name C or \ name O or name CB )) or resid 945 or (resid 946 and (name N or name CA or name C \ or name O or name CB )) or resid 947 through 948 or (resid 949 through 951 and \ (name N or name CA or name C or name O or name CB )) or resid 952 through 954 or \ (resid 955 through 957 and (name N or name CA or name C or name O or name CB )) \ or resid 958 through 959 or (resid 960 through 961 and (name N or name CA or na \ me C or name O or name CB )) or resid 962 or (resid 963 through 967 and (name N \ or name CA or name C or name O or name CB )) or resid 968 through 971 or (resid \ 972 and (name N or name CA or name C or name O or name CB )) or resid 973 throug \ h 974 or (resid 975 through 976 and (name N or name CA or name C or name O or na \ me CB )) or resid 977 through 995 or (resid 996 through 998 and (name N or name \ CA or name C or name O or name CB )) or resid 999 through 1026 or (resid 1027 an \ d (name N or name CA or name C or name O or name CB )) or resid 1028 through 103 \ 0 or (resid 1031 through 1033 and (name N or name CA or name C or name O or name \ CB )) or resid 1034 through 1051 or (resid 1052 through 1055 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1056 through 1077 or (resid 1078 \ and (name N or name CA or name C or name O or name CB )) or resid 1079 through \ 1089 or (resid 1090 and (name N or name CA or name C or name O or name CB )) or \ resid 1091 through 1092 or (resid 1093 and (name N or name CA or name C or name \ O or name CB )) or resid 1094 through 1095 or (resid 1096 through 1102 and (name \ N or name CA or name C or name O or name CB )) or resid 1103 through 1106 or (r \ esid 1107 and (name N or name CA or name C or name O or name CB )) or resid 1108 \ through 1109 or (resid 1110 through 1112 and (name N or name CA or name C or na \ me O or name CB )) or resid 1113 through 1116 or (resid 1117 and (name N or name \ CA or name C or name O or name CB )) or resid 1118 through 1310)) selection = (chain 'B' and (resid 18 through 21 or resid 31 through 46 or (resid 47 through \ 52 and (name N or name CA or name C or name O or name CB )) or resid 53 through \ 58 or (resid 59 through 60 and (name N or name CA or name C or name O or name CB \ )) or resid 61 through 157 or (resid 158 and (name N or name CA or name C or na \ me O or name CB )) or resid 159 through 168 or resid 179 through 257 or (resid 2 \ 58 through 265 and (name N or name CA or name C or name O or name CB )) or resid \ 266 through 280 or (resid 281 and (name N or name CA or name C or name O or nam \ e CB )) or resid 282 or (resid 283 through 286 and (name N or name CA or name C \ or name O or name CB )) or resid 287 through 290 or (resid 291 and (name N or na \ me CA or name C or name O or name CB )) or resid 292 through 293 or (resid 294 a \ nd (name N or name CA or name C or name O or name CB )) or resid 295 through 306 \ or (resid 307 through 308 and (name N or name CA or name C or name O or name CB \ )) or resid 309 through 529 or (resid 530 and (name N or name CA or name C or n \ ame O or name CB )) or resid 531 or (resid 532 through 533 and (name N or name C \ A or name C or name O or name CB )) or resid 534 or (resid 535 and (name N or na \ me CA or name C or name O or name CB )) or resid 536 through 542 or (resid 543 t \ hrough 544 and (name N or name CA or name C or name O or name CB )) or resid 545 \ through 552 or (resid 553 through 564 and (name N or name CA or name C or name \ O or name CB )) or resid 565 through 581 or (resid 582 through 585 and (name N o \ r name CA or name C or name O or name CB )) or resid 586 through 587 or (resid 5 \ 88 and (name N or name CA or name C or name O or name CB )) or resid 589 through \ 600 or (resid 601 and (name N or name CA or name C or name O or name CB )) or r \ esid 602 through 603 or (resid 604 through 616 and (name N or name CA or name C \ or name O or name CB )) or resid 617 through 627 or (resid 628 and (name N or na \ me CA or name C or name O or name CB )) or resid 629 through 630 or (resid 631 t \ hrough 633 and (name N or name CA or name C or name O or name CB )) or resid 634 \ through 635 or (resid 636 through 637 and (name N or name CA or name C or name \ O or name CB )) or (resid 638 through 645 and (name N or name CA or name C or na \ me O or name CB )) or resid 646 through 648 or (resid 649 through 650 and (name \ N or name CA or name C or name O or name CB )) or resid 651 or (resid 652 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 653 through 656 and \ (name N or name CA or name C or name O or name CB )) or resid 657 through 674 o \ r (resid 675 through 676 and (name N or name CA or name C or name O or name CB ) \ ) or resid 677 through 679 or (resid 680 and (name N or name CA or name C or nam \ e O or name CB )) or resid 681 through 684 or (resid 685 through 690 and (name N \ or name CA or name C or name O or name CB )) or resid 691 through 706 or (resid \ 707 and (name N or name CA or name C or name O or name CB )) or resid 708 throu \ gh 714 or (resid 715 through 716 and (name N or name CA or name C or name O or n \ ame CB )) or resid 717 through 728 or (resid 729 through 730 and (name N or name \ CA or name C or name O or name CB )) or resid 731 through 732 or (resid 733 thr \ ough 737 and (name N or name CA or name C or name O or name CB )) or resid 738 t \ hrough 754 or (resid 755 and (name N or name CA or name C or name O or name CB ) \ ) or resid 756 through 765 or (resid 766 and (name N or name CA or name C or nam \ e O or name CB )) or resid 767 or (resid 768 through 770 and (name N or name CA \ or name C or name O or name CB )) or resid 771 through 776 or (resid 777 and (na \ me N or name CA or name C or name O or name CB )) or resid 778 through 786 or (r \ esid 787 through 788 and (name N or name CA or name C or name O or name CB )) or \ resid 789 through 797 or (resid 798 and (name N or name CA or name C or name O \ or name CB )) or resid 799 or (resid 800 through 802 and (name N or name CA or n \ ame C or name O or name CB )) or resid 803 or (resid 804 and (name N or name CA \ or name C or name O or name CB )) or resid 805 through 808 or resid 819 through \ 839 or (resid 840 through 843 and (name N or name CA or name C or name O or name \ CB )) or resid 844 through 845 or (resid 846 and (name N or name CA or name C o \ r name O or name CB )) or resid 847 through 849 or (resid 850 and (name N or nam \ e CA or name C or name O or name CB )) or resid 851 through 860 or (resid 861 an \ d (name N or name CA or name C or name O or name CB )) or resid 862 through 864 \ or (resid 865 through 866 and (name N or name CA or name C or name O or name CB \ )) or resid 867 through 875 or (resid 876 through 877 and (name N or name CA or \ name C or name O or name CB )) or resid 878 through 881 or (resid 882 through 88 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 886 through \ 892 or (resid 893 through 895 and (name N or name CA or name C or name O or name \ CB )) or resid 896 through 902 or (resid 903 through 904 and (name N or name CA \ or name C or name O or name CB )) or resid 905 through 913 or (resid 914 throug \ h 915 and (name N or name CA or name C or name O or name CB )) or resid 916 or ( \ resid 917 through 919 and (name N or name CA or name C or name O or name CB )) o \ r resid 920 through 926 or (resid 927 and (name N or name CA or name C or name O \ or name CB )) or resid 928 through 930 or (resid 931 through 932 and (name N or \ name CA or name C or name O or name CB )) or resid 933 through 935 or (resid 93 \ 6 through 940 and (name N or name CA or name C or name O or name CB )) or resid \ 941 through 943 or (resid 944 and (name N or name CA or name C or name O or name \ CB )) or resid 945 through 950 or (resid 951 and (name N or name CA or name C o \ r name O or name CB )) or resid 952 through 964 or (resid 965 through 967 and (n \ ame N or name CA or name C or name O or name CB )) or resid 968 through 971 or ( \ resid 972 and (name N or name CA or name C or name O or name CB )) or resid 973 \ through 975 or (resid 976 and (name N or name CA or name C or name O or name CB \ )) or resid 977 through 995 or (resid 996 through 998 and (name N or name CA or \ name C or name O or name CB )) or resid 999 through 1002 or (resid 1003 through \ 1004 and (name N or name CA or name C or name O or name CB )) or resid 1005 thro \ ugh 1030 or (resid 1031 through 1033 and (name N or name CA or name C or name O \ or name CB )) or resid 1034 through 1051 or (resid 1052 through 1055 and (name N \ or name CA or name C or name O or name CB )) or resid 1056 through 1067 or (res \ id 1068 through 1069 and (name N or name CA or name C or name O or name CB )) or \ resid 1070 through 1077 or (resid 1078 and (name N or name CA or name C or name \ O or name CB )) or resid 1079 through 1085 or (resid 1086 through 1088 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1089 through 1096 or ( \ resid 1097 through 1102 and (name N or name CA or name C or name O or name CB )) \ or resid 1103 through 1104 or (resid 1105 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1106 through 1111 or (resid 1112 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1113 through 1309)) selection = (chain 'C' and (resid 18 through 21 or (resid 31 through 38 and (name N or name \ CA or name C or name O or name CB )) or resid 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 46 or (resid 47 throu \ gh 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throu \ gh 72 or (resid 73 through 78 and (name N or name CA or name C or name O or name \ CB )) or resid 79 through 87 or (resid 88 through 99 and (name N or name CA or \ name C or name O or name CB )) or resid 100 or (resid 101 through 103 and (name \ N or name CA or name C or name O or name CB )) or resid 104 through 184 or (resi \ d 185 through 191 and (name N or name CA or name C or name O or name CB )) or re \ sid 192 or (resid 193 through 198 and (name N or name CA or name C or name O or \ name CB )) or resid 199 through 212 or (resid 213 through 217 and (name N or nam \ e CA or name C or name O or name CB )) or resid 218 through 219 or (resid 220 th \ rough 222 and (name N or name CA or name C or name O or name CB )) or resid 223 \ through 237 or (resid 251 through 254 and (name N or name CA or name C or name O \ or name CB )) or resid 255 or (resid 256 through 265 and (name N or name CA or \ name C or name O or name CB )) or resid 266 through 270 or (resid 271 through 27 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 278 through \ 290 or (resid 291 and (name N or name CA or name C or name O or name CB )) or re \ sid 292 through 483 or resid 492 through 502 or resid 509 through 552 or (resid \ 553 through 564 and (name N or name CA or name C or name O or name CB )) or resi \ d 565 through 688 or (resid 689 through 690 and (name N or name CA or name C or \ name O or name CB )) or resid 691 through 706 or (resid 707 and (name N or name \ CA or name C or name O or name CB )) or resid 708 through 715 or (resid 716 and \ (name N or name CA or name C or name O or name CB )) or resid 717 or (resid 718 \ through 719 and (name N or name CA or name C or name O or name CB )) or resid 72 \ 0 through 723 or (resid 724 and (name N or name CA or name C or name O or name C \ B )) or resid 725 through 734 or (resid 735 through 737 and (name N or name CA o \ r name C or name O or name CB )) or resid 738 through 739 or (resid 740 and (nam \ e N or name CA or name C or name O or name CB )) or resid 741 through 743 or (re \ sid 744 and (name N or name CA or name C or name O or name CB )) or resid 745 th \ rough 765 or (resid 766 and (name N or name CA or name C or name O or name CB )) \ or resid 767 through 771 or (resid 772 and (name N or name CA or name C or name \ O or name CB )) or resid 773 through 801 or (resid 802 and (name N or name CA o \ r name C or name O or name CB )) or resid 803 through 883 or (resid 884 through \ 885 and (name N or name CA or name C or name O or name CB )) or resid 886 throug \ h 920 or (resid 921 through 927 and (name N or name CA or name C or name O or na \ me CB )) or resid 928 through 959 or (resid 960 through 961 and (name N or name \ CA or name C or name O or name CB )) or resid 962 through 1058 or (resid 1059 th \ rough 1060 and (name N or name CA or name C or name O or name CB )) or resid 106 \ 1 through 1092 or (resid 1093 and (name N or name CA or name C or name O or name \ CB )) or resid 1094 through 1106 or (resid 1107 and (name N or name CA or name \ C or name O or name CB )) or resid 1108 through 1109 or (resid 1110 through 1112 \ and (name N or name CA or name C or name O or name CB )) or resid 1113 through \ 1116 or (resid 1117 and (name N or name CA or name C or name O or name CB )) or \ resid 1118 through 1119 or (resid 1120 through 1121 and (name N or name CA or na \ me C or name O or name CB )) or resid 1122 through 1320)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'r' selection = chain 't' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'd' selection = chain 'q' } ncs_group { reference = chain 'T' selection = chain 'f' selection = chain 'g' selection = chain 's' } ncs_group { reference = chain 'W' selection = chain 'b' selection = chain 'i' selection = chain 'k' selection = chain 'o' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.270 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.130 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 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 : 0.016 0.149 25299 Z= 0.868 Angle : 1.537 19.794 35137 Z= 0.943 Chirality : 0.096 0.760 4608 Planarity : 0.006 0.037 4553 Dihedral : 9.017 89.202 6529 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.21 % Favored : 96.57 % Rotamer: Outliers : 0.97 % Allowed : 1.93 % Favored : 97.10 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 7.85 % 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 are not related in a simple way. whole: 0.24 (0.13), residues: 3764 helix: 0.39 (0.19), residues: 689 sheet: 0.73 (0.17), residues: 909 loop : -0.09 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 315 TYR 0.041 0.005 TYR B 778 PHE 0.024 0.004 PHE C 551 TRP 0.029 0.004 TRP C1084 HIS 0.006 0.001 HIS C 661 Details of bonding type rmsd/Z covalent geometry : bond 0.01576 / 0.86 (25111) covalent geometry : angle 1.49545 / 0.94 (34624) SS BOND : bond 0.02439 / 1.82 ( 51) SS BOND : angle 4.17228 / 2.84 ( 102) hydrogen bonds : bond 0.17714 / 12.88 ( 1278) hydrogen bonds : angle 8.26776 / 5.97 ( 3576) link_ALPHA1-3 : bond 0.03785 / 2.31 ( 8) link_ALPHA1-3 : angle 1.27681 / 0.86 ( 24) link_ALPHA1-6 : bond 0.02900 / 1.76 ( 8) link_ALPHA1-6 : angle 1.90766 / 1.22 ( 24) link_BETA1-4 : bond 0.03895 / 2.66 ( 68) link_BETA1-4 : angle 2.91133 / 1.99 ( 204) link_NAG-ASN : bond 0.03511 / 2.46 ( 53) link_NAG-ASN : angle 3.52133 / 2.55 ( 159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 248 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 LEU cc_start: 0.9035 (mp) cc_final: 0.8817 (mp) REVERT: B 269 ASN cc_start: 0.7145 (OUTLIER) cc_final: 0.6225 (p0) REVERT: B 649 ASP cc_start: 0.7994 (t0) cc_final: 0.7734 (t70) REVERT: B 650 ILE cc_start: 0.8027 (mt) cc_final: 0.7824 (tp) REVERT: B 770 MET cc_start: 0.7611 (mmm) cc_final: 0.7172 (mmm) REVERT: B 846 LEU cc_start: 0.8828 (tp) cc_final: 0.8226 (tp) REVERT: B 1046 HIS cc_start: 0.8740 (m-70) cc_final: 0.8039 (m-70) REVERT: C 700 PHE cc_start: 0.7762 (p90) cc_final: 0.7487 (p90) REVERT: C 713 MET cc_start: 0.8195 (ptt) cc_final: 0.7702 (ptm) REVERT: C 722 MET cc_start: 0.8749 (mmm) cc_final: 0.8479 (mmm) REVERT: C 888 PHE cc_start: 0.9077 (m-80) cc_final: 0.8825 (m-10) REVERT: C 988 THR cc_start: 0.9137 (m) cc_final: 0.8870 (p) REVERT: C 1000 ILE cc_start: 0.8792 (mt) cc_final: 0.8196 (mm) REVERT: C 1010 LYS cc_start: 0.9120 (mttm) cc_final: 0.8860 (mmtt) outliers start: 12 outliers final: 4 residues processed: 260 average time/residue: 0.1548 time to fit residues: 65.9771 Evaluate side-chains 126 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 GLN A 936 GLN A 937 ASN A1095 GLN B 993 GLN C1095 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.088945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.068371 restraints weight = 155240.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.069804 restraints weight = 92831.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.070791 restraints weight = 63938.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.071408 restraints weight = 49427.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.071858 restraints weight = 41777.191| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25299 Z= 0.160 Angle : 0.792 18.721 35137 Z= 0.364 Chirality : 0.051 0.594 4608 Planarity : 0.005 0.052 4553 Dihedral : 4.362 27.494 3920 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.10 % Favored : 97.87 % Rotamer: Outliers : 0.40 % Allowed : 1.77 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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 are not related in a simple way. whole: 0.71 (0.13), residues: 3764 helix: 1.55 (0.20), residues: 691 sheet: 0.68 (0.16), residues: 932 loop : 0.09 (0.13), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1089 TYR 0.022 0.002 TYR A1049 PHE 0.014 0.001 PHE A 870 TRP 0.016 0.002 TRP A 868 HIS 0.003 0.001 HIS B1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (25111) covalent geometry : angle 0.69245 / 0.34 (34624) SS BOND : bond 0.00367 / 0.27 ( 51) SS BOND : angle 1.44162 / 0.91 ( 102) hydrogen bonds : bond 0.05320 / 3.87 ( 1278) hydrogen bonds : angle 6.12619 / 4.49 ( 3576) link_ALPHA1-3 : bond 0.00648 / 0.39 ( 8) link_ALPHA1-3 : angle 1.96788 / 1.26 ( 24) link_ALPHA1-6 : bond 0.00848 / 0.53 ( 8) link_ALPHA1-6 : angle 1.57093 / 1.03 ( 24) link_BETA1-4 : bond 0.00736 / 0.51 ( 68) link_BETA1-4 : angle 3.22071 / 2.19 ( 204) link_NAG-ASN : bond 0.00869 / 0.65 ( 53) link_NAG-ASN : angle 4.30149 / 2.96 ( 159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 745 LEU cc_start: 0.9355 (tp) cc_final: 0.9079 (tt) REVERT: A 927 LEU cc_start: 0.8715 (mt) cc_final: 0.8504 (mt) REVERT: A 1042 VAL cc_start: 0.9183 (t) cc_final: 0.8905 (m) REVERT: A 1072 PRO cc_start: 0.8451 (Cg_endo) cc_final: 0.8084 (Cg_exo) REVERT: B 770 MET cc_start: 0.7507 (mmm) cc_final: 0.6865 (mmt) REVERT: B 846 LEU cc_start: 0.8749 (tp) cc_final: 0.8521 (tp) REVERT: B 983 LEU cc_start: 0.8644 (mt) cc_final: 0.8280 (mt) REVERT: B 1046 HIS cc_start: 0.8776 (m-70) cc_final: 0.7850 (m170) REVERT: C 700 PHE cc_start: 0.7726 (p90) cc_final: 0.7421 (p90) REVERT: C 713 MET cc_start: 0.8301 (ptt) cc_final: 0.7704 (ptm) REVERT: C 722 MET cc_start: 0.9085 (mmm) cc_final: 0.8863 (mmm) REVERT: C 888 PHE cc_start: 0.8952 (m-80) cc_final: 0.8560 (m-10) REVERT: C 988 THR cc_start: 0.9106 (m) cc_final: 0.8836 (p) REVERT: C 991 THR cc_start: 0.9023 (m) cc_final: 0.8777 (p) REVERT: C 1000 ILE cc_start: 0.9016 (mt) cc_final: 0.8694 (tp) REVERT: C 1046 HIS cc_start: 0.8680 (m-70) cc_final: 0.8149 (m-70) REVERT: C 1120 TYR cc_start: 0.8310 (m-80) cc_final: 0.7832 (m-80) outliers start: 5 outliers final: 2 residues processed: 167 average time/residue: 0.1308 time to fit residues: 38.3746 Evaluate side-chains 109 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 204 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 302 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 chunk 40 optimal weight: 30.0000 chunk 294 optimal weight: 4.9990 chunk 216 optimal weight: 9.9990 chunk 176 optimal weight: 0.6980 chunk 15 optimal weight: 0.0470 overall best weight: 2.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN A 987 GLN A1018 GLN B 908 GLN B 917 GLN B 987 GLN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 984 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.082087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.062493 restraints weight = 162740.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.061542 restraints weight = 118862.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.061850 restraints weight = 106355.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.061884 restraints weight = 106007.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.062041 restraints weight = 89349.593| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 25299 Z= 0.276 Angle : 0.890 20.058 35137 Z= 0.424 Chirality : 0.052 0.366 4608 Planarity : 0.006 0.087 4553 Dihedral : 4.743 24.871 3920 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 0.24 % Allowed : 4.99 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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 are not related in a simple way. whole: 0.09 (0.13), residues: 3764 helix: 0.72 (0.19), residues: 680 sheet: 0.43 (0.16), residues: 908 loop : -0.25 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 887 TYR 0.029 0.002 TYR B 723 PHE 0.024 0.002 PHE B 764 TRP 0.019 0.002 TRP A 619 HIS 0.011 0.003 HIS B1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.27 (25111) covalent geometry : angle 0.82631 / 0.41 (34624) SS BOND : bond 0.01136 / 0.68 ( 51) SS BOND : angle 2.08412 / 1.43 ( 102) hydrogen bonds : bond 0.05475 / 3.93 ( 1278) hydrogen bonds : angle 6.12917 / 4.46 ( 3576) link_ALPHA1-3 : bond 0.00824 / 0.50 ( 8) link_ALPHA1-3 : angle 1.70029 / 1.08 ( 24) link_ALPHA1-6 : bond 0.00935 / 0.58 ( 8) link_ALPHA1-6 : angle 1.44220 / 0.90 ( 24) link_BETA1-4 : bond 0.00729 / 0.50 ( 68) link_BETA1-4 : angle 2.96226 / 1.98 ( 204) link_NAG-ASN : bond 0.01044 / 0.73 ( 53) link_NAG-ASN : angle 3.37186 / 2.39 ( 159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 709 MET cc_start: 0.9042 (mtm) cc_final: 0.8611 (ptp) REVERT: A 770 MET cc_start: 0.7858 (mmt) cc_final: 0.7536 (mmm) REVERT: A 1011 MET cc_start: 0.8712 (tmm) cc_final: 0.8418 (tmm) REVERT: B 713 MET cc_start: 0.8888 (ptm) cc_final: 0.8380 (ptm) REVERT: B 723 TYR cc_start: 0.8398 (t80) cc_final: 0.8137 (t80) REVERT: B 770 MET cc_start: 0.7869 (mmm) cc_final: 0.7468 (mmm) REVERT: B 851 MET cc_start: 0.8846 (mtm) cc_final: 0.8609 (mtm) REVERT: B 972 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8716 (tm-30) REVERT: C 293 PHE cc_start: 0.7880 (m-80) cc_final: 0.7654 (m-10) REVERT: C 713 MET cc_start: 0.8451 (ptt) cc_final: 0.8111 (ptm) REVERT: C 722 MET cc_start: 0.9080 (mmm) cc_final: 0.8744 (tmm) REVERT: C 991 THR cc_start: 0.9170 (m) cc_final: 0.8943 (p) REVERT: C 1046 HIS cc_start: 0.9032 (m-70) cc_final: 0.8228 (m-70) REVERT: C 1120 TYR cc_start: 0.8603 (m-80) cc_final: 0.8206 (m-80) outliers start: 3 outliers final: 1 residues processed: 116 average time/residue: 0.1419 time to fit residues: 29.0854 Evaluate side-chains 87 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 128 optimal weight: 1.9990 chunk 348 optimal weight: 40.0000 chunk 145 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 chunk 247 optimal weight: 0.0370 chunk 378 optimal weight: 30.0000 chunk 227 optimal weight: 6.9990 chunk 225 optimal weight: 30.0000 chunk 194 optimal weight: 0.6980 chunk 14 optimal weight: 20.0000 chunk 266 optimal weight: 2.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 GLN B 992 GLN B1030 HIS ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.083929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.064770 restraints weight = 162059.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.064263 restraints weight = 117807.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.064248 restraints weight = 90049.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.064432 restraints weight = 97004.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.064501 restraints weight = 82469.475| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25299 Z= 0.124 Angle : 0.688 14.025 35137 Z= 0.314 Chirality : 0.048 0.418 4608 Planarity : 0.004 0.045 4553 Dihedral : 4.080 23.181 3920 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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 are not related in a simple way. whole: 0.44 (0.13), residues: 3764 helix: 1.65 (0.20), residues: 668 sheet: 0.39 (0.16), residues: 952 loop : -0.13 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1021 TYR 0.016 0.001 TYR B 723 PHE 0.025 0.001 PHE A 888 TRP 0.060 0.003 TRP C 868 HIS 0.003 0.001 HIS C1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (25111) covalent geometry : angle 0.61029 / 0.30 (34624) SS BOND : bond 0.00303 / 0.20 ( 51) SS BOND : angle 1.48759 / 0.96 ( 102) hydrogen bonds : bond 0.04289 / 3.09 ( 1278) hydrogen bonds : angle 5.32363 / 3.87 ( 3576) link_ALPHA1-3 : bond 0.00851 / 0.51 ( 8) link_ALPHA1-3 : angle 1.50539 / 0.98 ( 24) link_ALPHA1-6 : bond 0.00910 / 0.58 ( 8) link_ALPHA1-6 : angle 1.54819 / 1.00 ( 24) link_BETA1-4 : bond 0.00661 / 0.44 ( 68) link_BETA1-4 : angle 2.71752 / 1.84 ( 204) link_NAG-ASN : bond 0.00721 / 0.49 ( 53) link_NAG-ASN : angle 3.46865 / 2.50 ( 159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.846 Fit side-chains REVERT: A 850 ASP cc_start: 0.8111 (m-30) cc_final: 0.7825 (m-30) REVERT: A 1070 TYR cc_start: 0.6446 (m-80) cc_final: 0.6196 (m-10) REVERT: B 713 MET cc_start: 0.9064 (ptm) cc_final: 0.8497 (ptm) REVERT: B 723 TYR cc_start: 0.8480 (t80) cc_final: 0.8135 (t80) REVERT: B 755 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7938 (mm-30) REVERT: B 770 MET cc_start: 0.7643 (mmm) cc_final: 0.7214 (mmm) REVERT: B 851 MET cc_start: 0.8985 (mtm) cc_final: 0.8722 (ttm) REVERT: B 887 ARG cc_start: 0.8595 (mtt-85) cc_final: 0.6788 (mmt90) REVERT: B 972 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8753 (tm-30) REVERT: C 713 MET cc_start: 0.8321 (ptt) cc_final: 0.8065 (ptm) REVERT: C 722 MET cc_start: 0.8822 (mmm) cc_final: 0.8577 (tmm) REVERT: C 745 LEU cc_start: 0.9114 (tt) cc_final: 0.8873 (tt) REVERT: C 888 PHE cc_start: 0.8973 (m-10) cc_final: 0.8687 (m-80) REVERT: C 988 THR cc_start: 0.9031 (m) cc_final: 0.8693 (p) REVERT: C 991 THR cc_start: 0.8948 (m) cc_final: 0.8462 (p) REVERT: C 1000 ILE cc_start: 0.9168 (mt) cc_final: 0.8859 (tp) REVERT: C 1046 HIS cc_start: 0.9126 (m-70) cc_final: 0.8355 (m-70) REVERT: C 1120 TYR cc_start: 0.8480 (m-80) cc_final: 0.7789 (m-80) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1516 time to fit residues: 32.9958 Evaluate side-chains 98 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 121 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 175 optimal weight: 0.0170 chunk 151 optimal weight: 7.9990 chunk 299 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 330 optimal weight: 50.0000 chunk 156 optimal weight: 9.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 GLN A 641 HIS A 661 HIS ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN A1018 GLN C 721 ASN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.080062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.060718 restraints weight = 162395.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.060163 restraints weight = 120575.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.059865 restraints weight = 99604.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.060172 restraints weight = 102765.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.060359 restraints weight = 84977.816| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 25299 Z= 0.238 Angle : 0.797 16.145 35137 Z= 0.378 Chirality : 0.050 0.366 4608 Planarity : 0.005 0.079 4553 Dihedral : 4.520 23.046 3920 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.28 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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 are not related in a simple way. whole: 0.02 (0.13), residues: 3764 helix: 0.85 (0.19), residues: 678 sheet: 0.23 (0.16), residues: 901 loop : -0.28 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1021 TYR 0.036 0.002 TYR C 855 PHE 0.035 0.002 PHE C1044 TRP 0.038 0.004 TRP C 868 HIS 0.009 0.002 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.24 (25111) covalent geometry : angle 0.73513 / 0.36 (34624) SS BOND : bond 0.00470 / 0.32 ( 51) SS BOND : angle 1.78525 / 1.19 ( 102) hydrogen bonds : bond 0.04962 / 3.55 ( 1278) hydrogen bonds : angle 5.76388 / 4.18 ( 3576) link_ALPHA1-3 : bond 0.00723 / 0.43 ( 8) link_ALPHA1-3 : angle 1.81533 / 1.18 ( 24) link_ALPHA1-6 : bond 0.00902 / 0.57 ( 8) link_ALPHA1-6 : angle 1.47959 / 0.93 ( 24) link_BETA1-4 : bond 0.00692 / 0.47 ( 68) link_BETA1-4 : angle 2.83976 / 1.89 ( 204) link_NAG-ASN : bond 0.00829 / 0.59 ( 53) link_NAG-ASN : angle 3.05760 / 2.16 ( 159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 770 MET cc_start: 0.7548 (mmt) cc_final: 0.7182 (mmm) REVERT: A 850 ASP cc_start: 0.8245 (m-30) cc_final: 0.7937 (m-30) REVERT: B 713 MET cc_start: 0.8993 (ptm) cc_final: 0.8680 (ptm) REVERT: B 755 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7634 (mm-30) REVERT: B 770 MET cc_start: 0.7912 (mmm) cc_final: 0.7548 (mmm) REVERT: C 1046 HIS cc_start: 0.8992 (m-70) cc_final: 0.8372 (m-70) REVERT: C 1120 TYR cc_start: 0.8283 (m-80) cc_final: 0.7935 (m-80) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1467 time to fit residues: 27.9956 Evaluate side-chains 88 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 365 optimal weight: 1.9990 chunk 340 optimal weight: 50.0000 chunk 90 optimal weight: 0.6980 chunk 195 optimal weight: 0.7980 chunk 147 optimal weight: 20.0000 chunk 193 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 301 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 39 optimal weight: 0.0040 chunk 216 optimal weight: 9.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN ** C 756 GLN ** 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 = 0.3711 r_free = 0.3711 target = 0.081163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.060282 restraints weight = 154692.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.061585 restraints weight = 100717.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.061663 restraints weight = 70907.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.062239 restraints weight = 58464.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.062316 restraints weight = 49005.062| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25299 Z= 0.121 Angle : 0.666 10.942 35137 Z= 0.304 Chirality : 0.047 0.324 4608 Planarity : 0.004 0.044 4553 Dihedral : 3.970 22.288 3920 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.82 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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 are not related in a simple way. whole: 0.37 (0.14), residues: 3764 helix: 1.68 (0.20), residues: 670 sheet: 0.36 (0.16), residues: 913 loop : -0.21 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 758 TYR 0.014 0.001 TYR A 886 PHE 0.017 0.001 PHE A 548 TRP 0.021 0.002 TRP A 868 HIS 0.004 0.001 HIS B1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (25111) covalent geometry : angle 0.60090 / 0.29 (34624) SS BOND : bond 0.00341 / 0.24 ( 51) SS BOND : angle 1.43575 / 0.91 ( 102) hydrogen bonds : bond 0.04020 / 2.90 ( 1278) hydrogen bonds : angle 5.10796 / 3.70 ( 3576) link_ALPHA1-3 : bond 0.00826 / 0.50 ( 8) link_ALPHA1-3 : angle 1.46298 / 0.95 ( 24) link_ALPHA1-6 : bond 0.00931 / 0.60 ( 8) link_ALPHA1-6 : angle 1.53787 / 1.00 ( 24) link_BETA1-4 : bond 0.00639 / 0.43 ( 68) link_BETA1-4 : angle 2.63677 / 1.76 ( 204) link_NAG-ASN : bond 0.00508 / 0.35 ( 53) link_NAG-ASN : angle 2.92242 / 2.10 ( 159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.940 Fit side-chains REVERT: A 770 MET cc_start: 0.7264 (mmt) cc_final: 0.6968 (mmm) REVERT: A 850 ASP cc_start: 0.8142 (m-30) cc_final: 0.7887 (m-30) REVERT: A 1070 TYR cc_start: 0.6525 (m-80) cc_final: 0.6190 (m-10) REVERT: B 300 TYR cc_start: 0.8708 (m-80) cc_final: 0.8485 (m-80) REVERT: B 755 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7830 (mm-30) REVERT: B 882 MET cc_start: 0.8212 (mmp) cc_final: 0.7916 (mmp) REVERT: B 887 ARG cc_start: 0.8605 (mtt-85) cc_final: 0.7846 (mmt180) REVERT: C 722 MET cc_start: 0.7978 (tmm) cc_final: 0.7587 (tmm) REVERT: C 988 THR cc_start: 0.9081 (m) cc_final: 0.8730 (p) REVERT: C 1011 MET cc_start: 0.8822 (ttp) cc_final: 0.8263 (tmm) REVERT: C 1046 HIS cc_start: 0.9000 (m-70) cc_final: 0.8331 (m-70) REVERT: C 1120 TYR cc_start: 0.8093 (m-80) cc_final: 0.7410 (m-80) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1420 time to fit residues: 29.6303 Evaluate side-chains 85 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 343 optimal weight: 50.0000 chunk 324 optimal weight: 0.2980 chunk 123 optimal weight: 0.9990 chunk 274 optimal weight: 0.5980 chunk 127 optimal weight: 0.0000 chunk 361 optimal weight: 40.0000 chunk 360 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 317 optimal weight: 50.0000 chunk 161 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 744 GLN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.081334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.060611 restraints weight = 157164.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.061816 restraints weight = 105672.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.061794 restraints weight = 75377.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.062227 restraints weight = 63527.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.062308 restraints weight = 57162.360| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25299 Z= 0.125 Angle : 0.651 10.672 35137 Z= 0.298 Chirality : 0.046 0.299 4608 Planarity : 0.004 0.044 4553 Dihedral : 3.761 20.260 3920 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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 are not related in a simple way. whole: 0.49 (0.14), residues: 3764 helix: 1.86 (0.21), residues: 672 sheet: 0.37 (0.16), residues: 936 loop : -0.13 (0.14), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 747 TYR 0.017 0.001 TYR C 855 PHE 0.017 0.001 PHE A 741 TRP 0.016 0.002 TRP C 868 HIS 0.003 0.001 HIS C1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (25111) covalent geometry : angle 0.58766 / 0.28 (34624) SS BOND : bond 0.00305 / 0.22 ( 51) SS BOND : angle 1.46077 / 0.91 ( 102) hydrogen bonds : bond 0.03799 / 2.75 ( 1278) hydrogen bonds : angle 4.89642 / 3.54 ( 3576) link_ALPHA1-3 : bond 0.00707 / 0.43 ( 8) link_ALPHA1-3 : angle 1.56253 / 1.00 ( 24) link_ALPHA1-6 : bond 0.00934 / 0.60 ( 8) link_ALPHA1-6 : angle 1.43728 / 0.92 ( 24) link_BETA1-4 : bond 0.00636 / 0.43 ( 68) link_BETA1-4 : angle 2.57527 / 1.72 ( 204) link_NAG-ASN : bond 0.00470 / 0.31 ( 53) link_NAG-ASN : angle 2.81124 / 1.99 ( 159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 850 ASP cc_start: 0.8160 (m-30) cc_final: 0.7845 (m-30) REVERT: A 1070 TYR cc_start: 0.7170 (m-80) cc_final: 0.6660 (m-10) REVERT: B 755 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7703 (mm-30) REVERT: B 882 MET cc_start: 0.8441 (mmp) cc_final: 0.8118 (mmp) REVERT: C 988 THR cc_start: 0.9196 (m) cc_final: 0.8845 (p) REVERT: C 1011 MET cc_start: 0.8937 (ttp) cc_final: 0.8477 (tmm) REVERT: C 1046 HIS cc_start: 0.8954 (m-70) cc_final: 0.8231 (m-70) REVERT: C 1120 TYR cc_start: 0.8207 (m-80) cc_final: 0.7525 (m-80) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1429 time to fit residues: 26.5471 Evaluate side-chains 89 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 0.0170 chunk 233 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 252 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 303 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 142 optimal weight: 40.0000 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** 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 = 0.3668 r_free = 0.3668 target = 0.079113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.058429 restraints weight = 158107.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.059211 restraints weight = 108629.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.059162 restraints weight = 77319.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.059388 restraints weight = 70974.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.059544 restraints weight = 66882.088| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 25299 Z= 0.206 Angle : 0.735 11.894 35137 Z= 0.346 Chirality : 0.049 0.354 4608 Planarity : 0.004 0.047 4553 Dihedral : 4.189 21.698 3920 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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 are not related in a simple way. whole: 0.19 (0.14), residues: 3764 helix: 1.21 (0.20), residues: 685 sheet: 0.30 (0.17), residues: 920 loop : -0.24 (0.14), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1001 TYR 0.023 0.002 TYR B 771 PHE 0.025 0.002 PHE C1044 TRP 0.046 0.003 TRP C 868 HIS 0.007 0.002 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.21 (25111) covalent geometry : angle 0.68017 / 0.33 (34624) SS BOND : bond 0.00396 / 0.28 ( 51) SS BOND : angle 1.49821 / 0.97 ( 102) hydrogen bonds : bond 0.04475 / 3.22 ( 1278) hydrogen bonds : angle 5.37185 / 3.88 ( 3576) link_ALPHA1-3 : bond 0.00698 / 0.42 ( 8) link_ALPHA1-3 : angle 1.61338 / 1.04 ( 24) link_ALPHA1-6 : bond 0.00891 / 0.57 ( 8) link_ALPHA1-6 : angle 1.46453 / 0.93 ( 24) link_BETA1-4 : bond 0.00647 / 0.44 ( 68) link_BETA1-4 : angle 2.66713 / 1.77 ( 204) link_NAG-ASN : bond 0.00571 / 0.40 ( 53) link_NAG-ASN : angle 2.68395 / 1.85 ( 159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 850 ASP cc_start: 0.8274 (m-30) cc_final: 0.7984 (m-30) REVERT: A 1070 TYR cc_start: 0.7188 (m-80) cc_final: 0.6651 (m-10) REVERT: B 755 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 882 MET cc_start: 0.8517 (mmp) cc_final: 0.8242 (mmp) REVERT: C 713 MET cc_start: 0.8026 (ptp) cc_final: 0.7356 (ptm) REVERT: C 1011 MET cc_start: 0.9257 (ttp) cc_final: 0.8637 (tmm) REVERT: C 1046 HIS cc_start: 0.9105 (m-70) cc_final: 0.8610 (m-70) REVERT: C 1120 TYR cc_start: 0.8313 (m-80) cc_final: 0.7726 (m-80) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1360 time to fit residues: 24.9279 Evaluate side-chains 89 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 8.9990 chunk 372 optimal weight: 50.0000 chunk 246 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 131 optimal weight: 0.8980 chunk 242 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 289 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1030 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.077186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.057935 restraints weight = 163013.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.056636 restraints weight = 144017.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.056930 restraints weight = 120954.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.057092 restraints weight = 111950.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.057189 restraints weight = 99136.041| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.6467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 25299 Z= 0.292 Angle : 0.854 16.323 35137 Z= 0.408 Chirality : 0.051 0.480 4608 Planarity : 0.005 0.064 4553 Dihedral : 4.809 25.838 3920 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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 are not related in a simple way. whole: -0.33 (0.14), residues: 3764 helix: 0.33 (0.19), residues: 696 sheet: 0.13 (0.17), residues: 892 loop : -0.50 (0.14), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 887 TYR 0.030 0.003 TYR A 723 PHE 0.047 0.003 PHE C1044 TRP 0.039 0.004 TRP A 868 HIS 0.011 0.002 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.29 (25111) covalent geometry : angle 0.79905 / 0.40 (34624) SS BOND : bond 0.00500 / 0.36 ( 51) SS BOND : angle 1.87691 / 1.20 ( 102) hydrogen bonds : bond 0.05204 / 3.74 ( 1278) hydrogen bonds : angle 5.96601 / 4.31 ( 3576) link_ALPHA1-3 : bond 0.00726 / 0.44 ( 8) link_ALPHA1-3 : angle 1.73429 / 1.11 ( 24) link_ALPHA1-6 : bond 0.00895 / 0.57 ( 8) link_ALPHA1-6 : angle 1.49158 / 0.93 ( 24) link_BETA1-4 : bond 0.00681 / 0.46 ( 68) link_BETA1-4 : angle 2.86078 / 1.88 ( 204) link_NAG-ASN : bond 0.00628 / 0.45 ( 53) link_NAG-ASN : angle 2.91357 / 1.99 ( 159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.888 Fit side-chains REVERT: A 838 ASN cc_start: 0.8897 (p0) cc_final: 0.8524 (p0) REVERT: B 300 TYR cc_start: 0.8913 (m-80) cc_final: 0.8683 (m-80) REVERT: B 755 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8015 (mm-30) REVERT: B 851 MET cc_start: 0.9253 (mtm) cc_final: 0.9025 (mtm) REVERT: B 882 MET cc_start: 0.8832 (mmp) cc_final: 0.8509 (mmp) REVERT: B 972 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8850 (pp20) REVERT: C 679 MET cc_start: 0.8266 (ptm) cc_final: 0.7523 (ttp) REVERT: C 713 MET cc_start: 0.8290 (ptp) cc_final: 0.7615 (ptm) REVERT: C 797 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7112 (mtm180) REVERT: C 851 MET cc_start: 0.8307 (mpp) cc_final: 0.7857 (mpp) REVERT: C 1011 MET cc_start: 0.9372 (ttp) cc_final: 0.8741 (tmm) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1328 time to fit residues: 22.5488 Evaluate side-chains 80 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 50.0000 chunk 43 optimal weight: 0.0170 chunk 272 optimal weight: 1.9990 chunk 365 optimal weight: 50.0000 chunk 320 optimal weight: 50.0000 chunk 3 optimal weight: 0.6980 chunk 366 optimal weight: 30.0000 chunk 83 optimal weight: 0.6980 chunk 240 optimal weight: 50.0000 chunk 103 optimal weight: 3.9990 chunk 361 optimal weight: 40.0000 overall best weight: 1.4822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN ** C 756 GLN ** 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 = 0.3655 r_free = 0.3655 target = 0.078372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.059208 restraints weight = 161178.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.058289 restraints weight = 123696.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.058275 restraints weight = 106432.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.058385 restraints weight = 106739.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.058554 restraints weight = 92064.038| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.6514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25299 Z= 0.166 Angle : 0.736 12.842 35137 Z= 0.338 Chirality : 0.048 0.406 4608 Planarity : 0.005 0.056 4553 Dihedral : 4.368 20.895 3920 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.22 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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 are not related in a simple way. whole: -0.12 (0.14), residues: 3764 helix: 0.90 (0.19), residues: 698 sheet: 0.10 (0.17), residues: 904 loop : -0.43 (0.14), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 887 TYR 0.017 0.001 TYR C 855 PHE 0.027 0.002 PHE B 578 TRP 0.050 0.003 TRP B 868 HIS 0.006 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (25111) covalent geometry : angle 0.67691 / 0.32 (34624) SS BOND : bond 0.00369 / 0.25 ( 51) SS BOND : angle 1.78388 / 1.13 ( 102) hydrogen bonds : bond 0.04420 / 3.18 ( 1278) hydrogen bonds : angle 5.45755 / 3.94 ( 3576) link_ALPHA1-3 : bond 0.00784 / 0.47 ( 8) link_ALPHA1-3 : angle 1.60057 / 1.01 ( 24) link_ALPHA1-6 : bond 0.00911 / 0.58 ( 8) link_ALPHA1-6 : angle 1.45539 / 0.93 ( 24) link_BETA1-4 : bond 0.00638 / 0.43 ( 68) link_BETA1-4 : angle 2.67555 / 1.77 ( 204) link_NAG-ASN : bond 0.00461 / 0.31 ( 53) link_NAG-ASN : angle 2.84321 / 1.95 ( 159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 850 ASP cc_start: 0.8104 (m-30) cc_final: 0.7901 (m-30) REVERT: A 1070 TYR cc_start: 0.7140 (m-80) cc_final: 0.6673 (m-10) REVERT: B 300 TYR cc_start: 0.8861 (m-80) cc_final: 0.8551 (m-80) REVERT: B 755 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7961 (mm-30) REVERT: B 882 MET cc_start: 0.8646 (mmp) cc_final: 0.8154 (mmp) REVERT: C 679 MET cc_start: 0.8369 (ptm) cc_final: 0.7411 (ttp) REVERT: C 713 MET cc_start: 0.8224 (ptp) cc_final: 0.7529 (ptm) REVERT: C 988 THR cc_start: 0.9076 (m) cc_final: 0.8781 (p) REVERT: C 1011 MET cc_start: 0.9252 (ttp) cc_final: 0.8376 (tmm) REVERT: C 1046 HIS cc_start: 0.8857 (m-70) cc_final: 0.8234 (m-70) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1427 time to fit residues: 25.0928 Evaluate side-chains 87 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 322 optimal weight: 30.0000 chunk 244 optimal weight: 30.0000 chunk 255 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 217 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 370 optimal weight: 50.0000 chunk 102 optimal weight: 4.9990 chunk 236 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** 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 = 0.3615 r_free = 0.3615 target = 0.076575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.057201 restraints weight = 163179.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.056248 restraints weight = 130027.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.056459 restraints weight = 106484.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.056584 restraints weight = 105165.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.056647 restraints weight = 92286.808| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.7049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 25299 Z= 0.284 Angle : 0.851 15.849 35137 Z= 0.403 Chirality : 0.051 0.468 4608 Planarity : 0.005 0.067 4553 Dihedral : 4.794 26.390 3920 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.35 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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 are not related in a simple way. whole: -0.47 (0.14), residues: 3764 helix: 0.36 (0.19), residues: 703 sheet: -0.04 (0.17), residues: 893 loop : -0.61 (0.14), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 996 TYR 0.028 0.002 TYR C 886 PHE 0.042 0.003 PHE C1044 TRP 0.063 0.004 TRP C 868 HIS 0.009 0.002 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.28 (25111) covalent geometry : angle 0.79680 / 0.39 (34624) SS BOND : bond 0.00490 / 0.34 ( 51) SS BOND : angle 1.84712 / 1.18 ( 102) hydrogen bonds : bond 0.05074 / 3.66 ( 1278) hydrogen bonds : angle 5.97387 / 4.31 ( 3576) link_ALPHA1-3 : bond 0.00698 / 0.44 ( 8) link_ALPHA1-3 : angle 1.71453 / 1.07 ( 24) link_ALPHA1-6 : bond 0.00869 / 0.55 ( 8) link_ALPHA1-6 : angle 1.48248 / 0.93 ( 24) link_BETA1-4 : bond 0.00691 / 0.47 ( 68) link_BETA1-4 : angle 2.83130 / 1.87 ( 204) link_NAG-ASN : bond 0.00640 / 0.45 ( 53) link_NAG-ASN : angle 2.90649 / 1.97 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3383.97 seconds wall clock time: 59 minutes 15.73 seconds (3555.73 seconds total)