Starting phenix.real_space_refine on Sun Jul 5 10:08:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k9h_22748/07_2026/7k9h_22748.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k9h_22748/07_2026/7k9h_22748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7k9h_22748/07_2026/7k9h_22748.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k9h_22748/07_2026/7k9h_22748.cif" model { file = "/net/cci-nas-00/data/ceres_data/7k9h_22748/07_2026/7k9h_22748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k9h_22748/07_2026/7k9h_22748.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k9h_22748/07_2026/7k9h_22748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k9h_22748/07_2026/7k9h_22748.map" } resolution = 3.2 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= 0.002 sd= 0.076 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 112 5.16 5 C 17141 2.51 5 N 4388 2.21 5 O 5381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27022 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 6876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 950, 6876 Classifications: {'peptide': 950} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 47, 'TRANS': 902} Chain breaks: 12 Unresolved non-hydrogen bonds: 572 Unresolved non-hydrogen angles: 738 Unresolved non-hydrogen dihedrals: 477 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 382 Chain: "B" Number of atoms: 7649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7649 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 49, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 4, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 7623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7623 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 49, 'TRANS': 941} Chain breaks: 7 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 10, 'GLN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 80 Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "I" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 812 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "M" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 812 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "D" 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: "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: 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" 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: "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: "U" 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: "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: 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: "X" 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: 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: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: 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: 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: 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: "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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 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: "r" 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: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "u" 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: "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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.11, per 1000 atoms: 0.23 Number of scatterers: 27022 At special positions: 0 Unit cell: (132, 147.4, 202.4, 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 112 16.00 O 5381 8.00 N 4388 7.00 C 17141 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA P 3 " - " MAN P 4 " " BMA U 3 " - " MAN U 4 " " BMA r 3 " - " MAN r 4 " BETA1-4 " 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 G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " 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 m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " BETA1-6 " NAG J 1 " - " FUC J 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG b 1 " - " FUC b 2 " " NAG n 1 " - " FUC n 2 " NAG-ASN " NAG A1300 " - " ASN A 61 " " NAG B1300 " - " ASN B 61 " " NAG C1300 " - " ASN C 61 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 331 " " NAG J 1 " - " ASN A 603 " " NAG K 1 " - " ASN A 616 " " NAG N 1 " - " ASN A 657 " " NAG O 1 " - " ASN A 709 " " NAG P 1 " - " ASN A 717 " " NAG Q 1 " - " ASN A 801 " " NAG R 1 " - " ASN A1074 " " NAG S 1 " - " ASN A1098 " " NAG T 1 " - " ASN A1134 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 165 " " NAG W 1 " - " ASN B 234 " " NAG X 1 " - " ASN B 282 " " NAG Y 1 " - " ASN B 616 " " NAG Z 1 " - " ASN B 331 " " NAG a 1 " - " ASN B 343 " " NAG b 1 " - " ASN B 603 " " NAG c 1 " - " ASN B 657 " " NAG d 1 " - " ASN B 709 " " NAG e 1 " - " ASN B1098 " " NAG f 1 " - " ASN B 801 " " NAG g 1 " - " ASN B1074 " " NAG h 1 " - " ASN B1134 " " NAG i 1 " - " ASN C 165 " " NAG j 1 " - " ASN C 234 " " NAG k 1 " - " ASN C 282 " " NAG l 1 " - " ASN C 331 " " NAG m 1 " - " ASN C 343 " " NAG n 1 " - " ASN C 603 " " NAG o 1 " - " ASN C 616 " " NAG p 1 " - " ASN C 657 " " NAG q 1 " - " ASN C 709 " " NAG r 1 " - " ASN C 717 " " NAG s 1 " - " ASN C 801 " " NAG t 1 " - " ASN C1074 " " NAG u 1 " - " ASN C1098 " " NAG v 1 " - " ASN C1134 " Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 818.7 milliseconds 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6314 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 50 sheets defined 24.4% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.803A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.246A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.734A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.670A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.626A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.027A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.648A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.746A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.051A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.260A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.073A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.895A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.844A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.160A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.747A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.694A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.109A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.137A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.828A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.488A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.278A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.009A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.742A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.723A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.781A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.658A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.990A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.152A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.725A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.209A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.822A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.694A pdb=" N THR H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 90 removed outlier: 3.771A pdb=" N THR I 90 " --> pdb=" O THR I 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.701A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.457A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.736A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.944A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.922A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.854A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.070A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.070A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB3, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.889A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.658A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.571A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.746A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.845A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 325 through 328 removed outlier: 6.459A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.879A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.655A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.842A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AC7, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.779A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.249A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.699A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.632A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.606A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.970A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.574A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.598A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 451 through 454 removed outlier: 4.555A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR C 495 " --> pdb=" O TYR C 451 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.581A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.941A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.941A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.512A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER H 68 " --> pdb=" O LYS H 81 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.876A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR H 109 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.876A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.744A pdb=" N SER I 7 " --> pdb=" O THR I 21 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.582A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR I 109 " --> pdb=" O ARG I 97 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.524A pdb=" N THR L 5 " --> pdb=" O ARG L 23 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL L 18 " --> pdb=" O ILE L 77 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE L 77 " --> pdb=" O VAL L 18 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER L 67 " --> pdb=" O ALA L 74 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 9 through 10 removed outlier: 5.962A pdb=" N ALA L 35 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY L 51 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU L 45 " --> pdb=" O LYS L 41 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 9 through 10 Processing sheet with id=AF3, first strand: chain 'M' and resid 17 through 22 removed outlier: 3.585A pdb=" N ALA M 73 " --> pdb=" O CYS M 22 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER M 65 " --> pdb=" O THR M 76 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 55 through 56 removed outlier: 3.754A pdb=" N LEU M 45 " --> pdb=" O LYS M 41 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TRP M 37 " --> pdb=" O LEU M 49 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY M 51 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA M 35 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL M 99 " --> pdb=" O LEU M 92 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 55 through 56 removed outlier: 3.754A pdb=" N LEU M 45 " --> pdb=" O LYS M 41 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TRP M 37 " --> pdb=" O LEU M 49 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY M 51 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA M 35 " --> pdb=" O GLY M 51 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3036 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.12 Time building geometry restraints manager: 3.48 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: 5917 1.33 - 1.45: 6625 1.45 - 1.58: 14899 1.58 - 1.70: 2 1.70 - 1.82: 140 Bond restraints: 27583 Sorted by residual: bond pdb=" C1 NAG m 2 " pdb=" O5 NAG m 2 " ideal model delta sigma weight residual 1.406 1.495 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C1 NAG o 2 " pdb=" O5 NAG o 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG r 2 " pdb=" O5 NAG r 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C1 NAG s 2 " pdb=" O5 NAG s 2 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C1 NAG c 1 " pdb=" O5 NAG c 1 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 27578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 35935 1.77 - 3.54: 1361 3.54 - 5.31: 220 5.31 - 7.08: 72 7.08 - 8.86: 9 Bond angle restraints: 37597 Sorted by residual: angle pdb=" C PRO C 426 " pdb=" CA PRO C 426 " pdb=" CB PRO C 426 " ideal model delta sigma weight residual 110.98 104.20 6.78 1.31e+00 5.83e-01 2.68e+01 angle pdb=" C PRO C 561 " pdb=" N PHE C 562 " pdb=" CA PHE C 562 " ideal model delta sigma weight residual 121.54 130.40 -8.86 1.91e+00 2.74e-01 2.15e+01 angle pdb=" CA PHE C 429 " pdb=" CB PHE C 429 " pdb=" CG PHE C 429 " ideal model delta sigma weight residual 113.80 117.73 -3.93 1.00e+00 1.00e+00 1.54e+01 angle pdb=" CA ASP C 427 " pdb=" C ASP C 427 " pdb=" O ASP C 427 " ideal model delta sigma weight residual 121.19 116.87 4.32 1.10e+00 8.26e-01 1.54e+01 angle pdb=" N TYR B 91 " pdb=" CA TYR B 91 " pdb=" C TYR B 91 " ideal model delta sigma weight residual 109.07 103.89 5.18 1.61e+00 3.86e-01 1.03e+01 ... (remaining 37592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14206 17.94 - 35.87: 1048 35.87 - 53.81: 191 53.81 - 71.75: 47 71.75 - 89.68: 29 Dihedral angle restraints: 15521 sinusoidal: 5711 harmonic: 9810 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 -177.82 -89.18 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 178.64 -85.64 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -156.15 70.15 1 1.00e+01 1.00e-02 6.34e+01 ... (remaining 15518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 4621 0.181 - 0.362: 38 0.362 - 0.543: 3 0.543 - 0.724: 2 0.724 - 0.905: 1 Chirality restraints: 4665 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.61e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.66e+00 ... (remaining 4662 not shown) Planarity restraints: 4739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 64 " -0.028 2.00e-02 2.50e+03 2.08e-02 1.08e+01 pdb=" CG TRP B 64 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP B 64 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 64 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 64 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 64 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 64 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 64 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 64 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 64 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C1028 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.75e+00 pdb=" C LYS C1028 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS C1028 " -0.018 2.00e-02 2.50e+03 pdb=" N MET C1029 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 767 " 0.014 2.00e-02 2.50e+03 2.71e-02 7.35e+00 pdb=" C LEU B 767 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU B 767 " 0.017 2.00e-02 2.50e+03 pdb=" N THR B 768 " 0.016 2.00e-02 2.50e+03 ... (remaining 4736 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 509 2.65 - 3.21: 25431 3.21 - 3.77: 39942 3.77 - 4.34: 53811 4.34 - 4.90: 90929 Nonbonded interactions: 210622 Sorted by model distance: nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.085 3.040 nonbonded pdb=" NZ LYS B 378 " pdb=" OH TYR B 380 " model vdw 2.152 3.120 nonbonded pdb=" NZ LYS C 733 " pdb=" OD2 ASP C 775 " model vdw 2.171 3.120 nonbonded pdb=" NE2 GLN I 6 " pdb=" O TYR I 93 " model vdw 2.192 3.120 nonbonded pdb=" OG1 THR M 82 " pdb=" OE1 GLU M 83 " model vdw 2.203 3.040 ... (remaining 210617 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 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 throug \ h 109 or (resid 110 through 112 and (name N or name CA or name C or name O or na \ me CB )) or resid 113 through 128 or (resid 129 and (name N or name CA or name C \ or name O or name CB )) or resid 130 through 134 or (resid 135 through 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 140 or \ resid 165 through 168 or (resid 169 and (name N or name CA or name C or name O \ or name CB )) or resid 170 through 187 or (resid 188 and (name N or name CA or n \ ame C or name O or name CB )) or resid 189 through 190 or (resid 191 and (name N \ or name CA or name C or name O or name CB )) or resid 192 through 195 or (resid \ 196 and (name N or name CA or name C or name O or name CB )) or resid 200 throu \ gh 210 or (resid 211 through 215 and (name N or name CA or name C or name O or n \ ame CB )) or resid 216 through 241 or (resid 242 through 263 and (name N or name \ CA or name C or name O or name CB )) or resid 265 through 280 or (resid 281 and \ (name N or name CA or name C or name O or name CB )) or resid 282 through 323 o \ r (resid 324 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 25 through 567 or (resid 568 and (name N or name CA or name C or name O or name \ CB )) or resid 569 through 570 or (resid 571 and (name N or name CA or name C or \ name O or name CB )) or resid 572 through 581 or (resid 582 through 583 and (na \ me N or name CA or name C or name O or name CB )) or resid 584 through 585 or (r \ esid 586 and (name N or name CA or name C or name O or name CB )) or resid 587 t \ hrough 613 or (resid 614 and (name N or name CA or name C or name O or name CB ) \ ) or resid 615 through 618 or (resid 619 and (name N or name CA or name C or nam \ e O or name CB )) or resid 620 through 676 or resid 690 through 744 or (resid 74 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 746 through \ 810 or (resid 811 and (name N or name CA or name C or name O or name CB )) or re \ sid 812 through 827 or resid 856 through 866 or (resid 867 through 868 and (name \ N or name CA or name C or name O or name CB )) or resid 869 through 920 or (res \ id 921 and (name N or name CA or name C or name O or name CB )) or resid 922 thr \ ough 939 or (resid 940 and (name N or name CA or name C or name O or name CB )) \ or resid 941 through 984 or (resid 985 and (name N or name CA or name C or name \ O or name CB )) or resid 986 through 987 or (resid 988 through 989 and (name N o \ r name CA or name C or name O or name CB )) or resid 990 through 1117 or (resid \ 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 thro \ ugh 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name O \ or name CB )) or resid 1147 through 1300)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 through 112 and (name N or name CA o \ r name C or name O or name CB )) or resid 113 through 131 or (resid 132 and (nam \ e N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 thro \ ugh 138 and (name N or name CA or name C or name O or name CB )) or resid 139 th \ rough 140 or resid 165 through 168 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 171 or (resid 172 and (name N or \ name CA or name C or name O or name CB )) or resid 186 through 190 or (resid 191 \ and (name N or name CA or name C or name O or name CB )) or resid 192 through 1 \ 96 or resid 200 through 210 or (resid 211 and (name N or name CA or name C or na \ me O or name CB )) or (resid 215 and (name N or name CA or name C or name O or n \ ame CB )) or resid 216 through 217 or (resid 218 and (name N or name CA or name \ C or name O or name CB )) or resid 219 through 223 or (resid 224 and (name N or \ name CA or name C or name O or name CB )) or resid 225 through 238 or (resid 239 \ and (name N or name CA or name C or name O or name CB )) or resid 240 through 2 \ 63 or resid 265 through 308 or (resid 309 and (name N or name CA or name C or na \ me O or name CB )) or resid 310 through 323 or (resid 324 and (name N or name CA \ or name C or name O or name CB )) or resid 325 through 332 or (resid 333 throug \ h 334 and (name N or name CA or name C or name O or name CB )) or resid 335 thro \ ugh 339 or (resid 340 and (name N or name CA or name C or name O or name CB )) o \ r resid 341 through 344 or (resid 345 through 360 and (name N or name CA or name \ C or name O or name CB )) or resid 361 or (resid 362 through 378 and (name N or \ name CA or name C or name O or name CB )) or resid 379 or (resid 380 and (name \ N or name CA or name C or name O or name CB )) or resid 381 or (resid 382 throug \ h 383 and (name N or name CA or name C or name O or name CB )) or resid 384 or ( \ resid 385 through 390 and (name N or name CA or name C or name O or name CB )) o \ r resid 391 or (resid 392 through 403 and (name N or name CA or name C or name O \ or name CB )) or resid 404 or (resid 405 through 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 through 41 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 416 or (resi \ d 417 through 425 and (name N or name CA or name C or name O or name CB )) or re \ sid 426 or (resid 427 through 430 and (name N or name CA or name C or name O or \ name CB )) or resid 431 through 432 or (resid 433 through 445 and (name N or nam \ e CA or name C or name O or name CB )) or resid 446 through 447 or (resid 448 th \ rough 454 and (name N or name CA or name C or name O or name CB )) or (resid 462 \ and (name N or name CA or name C or name O or name CB )) or resid 463 or (resid \ 464 through 466 and (name N or name CA or name C or name O or name CB )) or res \ id 491 or (resid 492 through 495 and (name N or name CA or name C or name O or n \ ame CB )) or resid 496 or (resid 497 through 498 and (name N or name CA or name \ C or name O or name CB )) or resid 499 or (resid 500 through 501 and (name N or \ name CA or name C or name O or name CB )) or resid 502 or (resid 503 and (name N \ or name CA or name C or name O or name CB )) or resid 504 or (resid 505 through \ 506 and (name N or name CA or name C or name O or name CB )) or resid 507 or (r \ esid 508 through 515 and (name N or name CA or name C or name O or name CB )) or \ (resid 522 through 524 and (name N or name CA or name C or name O or name CB )) \ or resid 525 through 528 or (resid 529 and (name N or name CA or name C or name \ O or name CB )) or resid 530 through 553 or (resid 554 and (name N or name CA o \ r name C or name O or name CB )) or resid 555 through 793 or (resid 794 and (nam \ e N or name CA or name C or name O or name CB )) or resid 795 or (resid 796 and \ (name N or name CA or name C or name O or name CB )) or resid 797 through 810 or \ (resid 811 and (name N or name CA or name C or name O or name CB )) or resid 81 \ 2 through 866 or (resid 867 through 868 and (name N or name CA or name C or name \ O or name CB )) or resid 869 through 939 or (resid 940 and (name N or name CA o \ r name C or name O or name CB )) or resid 941 through 984 or (resid 985 and (nam \ e N or name CA or name C or name O or name CB )) or resid 986 through 987 or (re \ sid 988 through 989 and (name N or name CA or name C or name O or name CB )) or \ resid 990 through 1141 or (resid 1142 and (name N or name CA or name C or name O \ or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name \ N or name CA or name C or name O or name CB )) or resid 1147 through 1300)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 through 110 or (resid 111 through 112 and (name N or name CA or name C or n \ ame O or name CB )) or resid 113 through 128 or (resid 129 and (name N or name C \ A or name C or name O or name CB )) or resid 130 through 134 or (resid 135 throu \ gh 138 and (name N or name CA or name C or name O or name CB )) or resid 139 thr \ ough 140 or resid 165 through 187 or (resid 188 and (name N or name CA or name C \ or name O or name CB )) or resid 189 through 195 or (resid 196 and (name N or n \ ame CA or name C or name O or name CB )) or resid 200 through 211 or resid 215 t \ hrough 217 or (resid 218 and (name N or name CA or name C or name O or name CB ) \ ) or resid 219 through 223 or (resid 224 and (name N or name CA or name C or nam \ e O or name CB )) or resid 225 through 238 or (resid 239 and (name N or name CA \ or name C or name O or name CB )) or resid 240 through 308 or (resid 309 and (na \ me N or name CA or name C or name O or name CB )) or resid 310 through 332 or (r \ esid 333 through 334 and (name N or name CA or name C or name O or name CB )) or \ resid 335 through 339 or (resid 340 and (name N or name CA or name C or name O \ or name CB )) or resid 341 through 344 or (resid 345 through 360 and (name N or \ name CA or name C or name O or name CB )) or resid 361 or (resid 362 through 378 \ and (name N or name CA or name C or name O or name CB )) or resid 379 or (resid \ 380 and (name N or name CA or name C or name O or name CB )) or resid 381 or (r \ esid 382 through 383 and (name N or name CA or name C or name O or name CB )) or \ resid 384 or (resid 385 through 390 and (name N or name CA or name C or name O \ or name CB )) or resid 391 or (resid 392 through 403 and (name N or name CA or n \ ame C or name O or name CB )) or resid 404 or (resid 405 through 411 and (name N \ or name CA or name C or name O or name CB )) or resid 412 through 413 or (resid \ 414 through 415 and (name N or name CA or name C or name O or name CB )) or res \ id 416 or (resid 417 through 425 and (name N or name CA or name C or name O or n \ ame CB )) or resid 426 or (resid 427 through 430 and (name N or name CA or name \ C or name O or name CB )) or resid 431 through 432 or (resid 433 through 445 and \ (name N or name CA or name C or name O or name CB )) or resid 446 through 447 o \ r (resid 448 through 454 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 462 and (name N or name CA or name C or name O or name CB )) or resi \ d 463 or (resid 464 through 466 and (name N or name CA or name C or name O or na \ me CB )) or resid 491 or (resid 492 through 495 and (name N or name CA or name C \ or name O or name CB )) or resid 496 or (resid 497 through 498 and (name N or n \ ame CA or name C or name O or name CB )) or resid 499 or (resid 500 through 501 \ and (name N or name CA or name C or name O or name CB )) or resid 502 or (resid \ 503 and (name N or name CA or name C or name O or name CB )) or resid 504 or (re \ sid 505 through 506 and (name N or name CA or name C or name O or name CB )) or \ resid 507 or (resid 508 through 515 and (name N or name CA or name C or name O o \ r name CB )) or (resid 522 through 524 and (name N or name CA or name C or name \ O or name CB )) or resid 525 through 527 or (resid 528 through 529 and (name N o \ r name CA or name C or name O or name CB )) or resid 530 through 553 or (resid 5 \ 54 and (name N or name CA or name C or name O or name CB )) or resid 555 through \ 567 or (resid 568 and (name N or name CA or name C or name O or name CB )) or r \ esid 569 through 570 or (resid 571 and (name N or name CA or name C or name O or \ name CB )) or resid 572 through 581 or (resid 582 through 583 and (name N or na \ me CA or name C or name O or name CB )) or resid 584 through 585 or (resid 586 a \ nd (name N or name CA or name C or name O or name CB )) or resid 587 through 618 \ or (resid 619 and (name N or name CA or name C or name O or name CB )) or resid \ 620 through 645 or (resid 646 through 647 and (name N or name CA or name C or n \ ame O or name CB )) or resid 648 through 793 or (resid 794 and (name N or name C \ A or name C or name O or name CB )) or resid 795 or (resid 796 and (name N or na \ me CA or name C or name O or name CB )) or resid 797 through 920 or (resid 921 a \ nd (name N or name CA or name C or name O or name CB )) or resid 922 through 111 \ 7 or (resid 1118 and (name N or name CA or name C or name O or name CB )) or res \ id 1119 through 1141 or (resid 1142 and (name N or name CA or name C or name O o \ r name CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name CA or \ name C or name O or name CB )) or resid 1147 through 1300)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'a' selection = chain 'e' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'm' selection = chain 'u' selection = chain 'v' } ncs_group { reference = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'k' and resid 1) selection = (chain 'l' and resid 1) selection = (chain 'n' and resid 1) selection = (chain 'o' and resid 1) selection = (chain 'p' and resid 1) selection = (chain 'q' and resid 1) selection = (chain 's' and resid 1) selection = (chain 't' and resid 1) } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.000 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.080 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 : 0.007 0.089 27730 Z= 0.305 Angle : 0.885 17.827 37996 Z= 0.431 Chirality : 0.059 0.905 4665 Planarity : 0.005 0.066 4695 Dihedral : 13.679 89.681 9081 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.18 % Allowed : 1.10 % Favored : 98.72 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.14), residues: 3325 helix: 1.29 (0.19), residues: 694 sheet: 0.01 (0.17), residues: 932 loop : -1.42 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 355 TYR 0.039 0.002 TYR B 495 PHE 0.036 0.002 PHE C 559 TRP 0.057 0.002 TRP B 64 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.30 (27583) covalent geometry : angle 0.83109 / 0.42 (37597) SS BOND : bond 0.00426 / 0.31 ( 42) SS BOND : angle 1.38949 / 0.88 ( 84) hydrogen bonds : bond 0.14674 / 9.47 ( 1090) hydrogen bonds : angle 7.30608 / 5.29 ( 3036) link_ALPHA1-6 : bond 0.00337 / 0.15 ( 3) link_ALPHA1-6 : angle 1.52802 / 0.83 ( 9) link_BETA1-4 : bond 0.01120 / 0.75 ( 55) link_BETA1-4 : angle 2.77473 / 1.99 ( 165) link_BETA1-6 : bond 0.00421 / 0.17 ( 3) link_BETA1-6 : angle 1.30489 / 0.76 ( 9) link_NAG-ASN : bond 0.00612 / 0.38 ( 44) link_NAG-ASN : angle 4.20415 / 2.63 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 206 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 708 SER cc_start: 0.7827 (t) cc_final: 0.7596 (m) REVERT: B 200 TYR cc_start: 0.7402 (m-80) cc_final: 0.7197 (m-10) REVERT: B 408 ARG cc_start: 0.8769 (tmm160) cc_final: 0.8445 (tmm160) REVERT: B 505 TYR cc_start: 0.8748 (m-10) cc_final: 0.8432 (m-80) REVERT: C 429 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8501 (t80) REVERT: H 36 TRP cc_start: 0.5978 (m100) cc_final: 0.5085 (m100) REVERT: H 63 LEU cc_start: 0.6825 (tp) cc_final: 0.6268 (mm) REVERT: H 73 ASN cc_start: 0.7343 (m110) cc_final: 0.7047 (m-40) REVERT: H 80 LEU cc_start: 0.7599 (tt) cc_final: 0.7274 (mt) REVERT: H 93 TYR cc_start: 0.7433 (m-80) cc_final: 0.6904 (m-10) REVERT: H 95 CYS cc_start: 0.5168 (p) cc_final: 0.4619 (p) REVERT: H 99 ASP cc_start: 0.6948 (t0) cc_final: 0.6609 (p0) REVERT: I 98 LYS cc_start: 0.5836 (mtmt) cc_final: 0.5524 (mtmt) REVERT: I 108 ASP cc_start: 0.4951 (t70) cc_final: 0.4275 (t0) REVERT: L 36 ASN cc_start: 0.6643 (m-40) cc_final: 0.6319 (t0) REVERT: M 49 LEU cc_start: 0.6468 (mt) cc_final: 0.6227 (tp) REVERT: M 92 LEU cc_start: 0.8587 (mp) cc_final: 0.8289 (mm) REVERT: M 96 ASN cc_start: 0.5439 (p0) cc_final: 0.4631 (t0) outliers start: 5 outliers final: 1 residues processed: 209 average time/residue: 0.1686 time to fit residues: 58.7688 Evaluate side-chains 164 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 514 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.1980 chunk 298 optimal weight: 9.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 957 GLN B1106 GLN H 73 ASN L 6 GLN L 96 ASN ** M 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.153712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.097656 restraints weight = 45180.330| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.20 r_work: 0.3252 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27730 Z= 0.135 Angle : 0.706 17.004 37996 Z= 0.335 Chirality : 0.051 0.589 4665 Planarity : 0.004 0.046 4695 Dihedral : 4.867 31.252 3599 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.66 % Allowed : 7.33 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3325 helix: 2.05 (0.20), residues: 689 sheet: 0.08 (0.17), residues: 915 loop : -1.17 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 403 TYR 0.026 0.001 TYR M 94 PHE 0.029 0.001 PHE C 559 TRP 0.031 0.002 TRP H 47 HIS 0.004 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (27583) covalent geometry : angle 0.65457 / 0.32 (37597) SS BOND : bond 0.00344 / 0.26 ( 42) SS BOND : angle 1.07600 / 0.64 ( 84) hydrogen bonds : bond 0.04826 / 3.13 ( 1090) hydrogen bonds : angle 5.88202 / 4.21 ( 3036) link_ALPHA1-6 : bond 0.00492 / 0.23 ( 3) link_ALPHA1-6 : angle 1.46873 / 0.85 ( 9) link_BETA1-4 : bond 0.01103 / 0.72 ( 55) link_BETA1-4 : angle 2.45582 / 1.78 ( 165) link_BETA1-6 : bond 0.00514 / 0.23 ( 3) link_BETA1-6 : angle 1.22097 / 0.69 ( 9) link_NAG-ASN : bond 0.00670 / 0.42 ( 44) link_NAG-ASN : angle 3.61696 / 2.26 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 775 ASP cc_start: 0.8184 (m-30) cc_final: 0.7955 (m-30) REVERT: B 200 TYR cc_start: 0.7777 (m-80) cc_final: 0.7391 (m-10) REVERT: B 214 ARG cc_start: 0.8445 (mmm160) cc_final: 0.8146 (mmm160) REVERT: B 408 ARG cc_start: 0.8752 (tmm160) cc_final: 0.8387 (tmm160) REVERT: B 955 ASN cc_start: 0.8202 (m110) cc_final: 0.7995 (m-40) REVERT: C 984 LEU cc_start: 0.8506 (tt) cc_final: 0.8199 (tt) REVERT: H 36 TRP cc_start: 0.5833 (m100) cc_final: 0.5395 (m100) REVERT: H 77 GLN cc_start: 0.9038 (pt0) cc_final: 0.8584 (pp30) REVERT: H 93 TYR cc_start: 0.6820 (m-80) cc_final: 0.6462 (m-10) REVERT: H 99 ASP cc_start: 0.6894 (t0) cc_final: 0.6369 (p0) REVERT: I 31 ASN cc_start: 0.8432 (t0) cc_final: 0.7497 (p0) REVERT: L 36 ASN cc_start: 0.6732 (m-40) cc_final: 0.6510 (t0) REVERT: L 94 TYR cc_start: 0.7908 (m-10) cc_final: 0.7646 (m-10) outliers start: 18 outliers final: 7 residues processed: 194 average time/residue: 0.1753 time to fit residues: 55.8085 Evaluate side-chains 171 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain L residue 55 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 6 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 92 optimal weight: 0.0770 chunk 95 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 957 GLN B1106 GLN L 6 GLN L 39 GLN L 55 ASN ** M 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.152465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.096212 restraints weight = 45269.525| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.96 r_work: 0.3192 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27730 Z= 0.163 Angle : 0.679 16.811 37996 Z= 0.320 Chirality : 0.051 0.579 4665 Planarity : 0.004 0.045 4695 Dihedral : 4.617 26.476 3596 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.32 % Allowed : 9.57 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.14), residues: 3325 helix: 2.10 (0.20), residues: 691 sheet: 0.14 (0.17), residues: 895 loop : -1.18 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 92 TYR 0.024 0.001 TYR M 94 PHE 0.032 0.001 PHE C 559 TRP 0.023 0.001 TRP H 47 HIS 0.004 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (27583) covalent geometry : angle 0.62707 / 0.31 (37597) SS BOND : bond 0.00503 / 0.39 ( 42) SS BOND : angle 1.20946 / 0.74 ( 84) hydrogen bonds : bond 0.04706 / 3.05 ( 1090) hydrogen bonds : angle 5.53999 / 3.98 ( 3036) link_ALPHA1-6 : bond 0.00420 / 0.18 ( 3) link_ALPHA1-6 : angle 1.44786 / 0.81 ( 9) link_BETA1-4 : bond 0.01026 / 0.66 ( 55) link_BETA1-4 : angle 2.38897 / 1.72 ( 165) link_BETA1-6 : bond 0.00503 / 0.22 ( 3) link_BETA1-6 : angle 1.20131 / 0.68 ( 9) link_NAG-ASN : bond 0.00602 / 0.36 ( 44) link_NAG-ASN : angle 3.51291 / 2.19 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 697 MET cc_start: 0.9059 (ptm) cc_final: 0.8802 (ptp) REVERT: B 200 TYR cc_start: 0.7847 (m-80) cc_final: 0.7530 (m-80) REVERT: B 214 ARG cc_start: 0.8628 (mmm160) cc_final: 0.8178 (mmm160) REVERT: B 408 ARG cc_start: 0.8753 (tmm160) cc_final: 0.8407 (tmm160) REVERT: B 990 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: C 408 ARG cc_start: 0.8323 (ttp80) cc_final: 0.8066 (ttp80) REVERT: C 984 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8076 (tt) REVERT: C 1050 MET cc_start: 0.8787 (ptm) cc_final: 0.8568 (ptm) REVERT: H 36 TRP cc_start: 0.5551 (m100) cc_final: 0.5211 (m100) REVERT: H 77 GLN cc_start: 0.8938 (pt0) cc_final: 0.8504 (pm20) REVERT: H 80 LEU cc_start: 0.7733 (tt) cc_final: 0.7233 (mt) REVERT: I 99 ASP cc_start: 0.4666 (p0) cc_final: 0.3962 (p0) REVERT: L 36 ASN cc_start: 0.6945 (m-40) cc_final: 0.6691 (t0) REVERT: M 94 TYR cc_start: 0.8466 (t80) cc_final: 0.8078 (t80) outliers start: 36 outliers final: 13 residues processed: 196 average time/residue: 0.1689 time to fit residues: 54.9735 Evaluate side-chains 174 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 30.0000 chunk 135 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 313 optimal weight: 50.0000 chunk 245 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 804 GLN B 901 GLN H 58 ASN ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 ASN L 96 ASN M 36 ASN ** M 81 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 = 0.4094 r_free = 0.4094 target = 0.148800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.092476 restraints weight = 45436.274| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.90 r_work: 0.3120 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 27730 Z= 0.319 Angle : 0.758 17.314 37996 Z= 0.363 Chirality : 0.054 0.562 4665 Planarity : 0.004 0.045 4695 Dihedral : 4.794 22.231 3596 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.54 % Allowed : 11.51 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3325 helix: 1.72 (0.20), residues: 691 sheet: -0.07 (0.17), residues: 917 loop : -1.30 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 97 TYR 0.029 0.002 TYR M 94 PHE 0.047 0.002 PHE C 559 TRP 0.024 0.002 TRP H 47 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00772 / 0.32 (27583) covalent geometry : angle 0.71100 / 0.35 (37597) SS BOND : bond 0.00436 / 0.32 ( 42) SS BOND : angle 1.38414 / 0.86 ( 84) hydrogen bonds : bond 0.05540 / 3.60 ( 1090) hydrogen bonds : angle 5.68819 / 4.08 ( 3036) link_ALPHA1-6 : bond 0.00326 / 0.15 ( 3) link_ALPHA1-6 : angle 1.51850 / 0.86 ( 9) link_BETA1-4 : bond 0.01007 / 0.66 ( 55) link_BETA1-4 : angle 2.38263 / 1.74 ( 165) link_BETA1-6 : bond 0.00406 / 0.17 ( 3) link_BETA1-6 : angle 1.28877 / 0.73 ( 9) link_NAG-ASN : bond 0.00575 / 0.35 ( 44) link_NAG-ASN : angle 3.58186 / 2.23 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7487 (m-80) cc_final: 0.6656 (m-80) REVERT: A 697 MET cc_start: 0.9125 (ptm) cc_final: 0.8883 (ptp) REVERT: B 200 TYR cc_start: 0.7954 (m-80) cc_final: 0.7696 (m-80) REVERT: B 214 ARG cc_start: 0.8706 (mmm160) cc_final: 0.8199 (mmm160) REVERT: B 408 ARG cc_start: 0.8758 (tmm160) cc_final: 0.8468 (tmm160) REVERT: B 752 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8870 (mp) REVERT: B 990 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: C 408 ARG cc_start: 0.8312 (ttp80) cc_final: 0.8054 (ttp80) REVERT: C 869 MET cc_start: 0.8664 (mtt) cc_final: 0.8396 (mtt) REVERT: C 984 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8062 (tt) REVERT: C 1050 MET cc_start: 0.8834 (ptm) cc_final: 0.8608 (ptm) REVERT: H 16 GLN cc_start: 0.4843 (OUTLIER) cc_final: 0.4372 (pm20) REVERT: H 36 TRP cc_start: 0.5583 (m100) cc_final: 0.5042 (m100) REVERT: H 77 GLN cc_start: 0.8968 (pt0) cc_final: 0.8570 (pm20) REVERT: H 80 LEU cc_start: 0.7844 (tt) cc_final: 0.7542 (tp) REVERT: I 32 TYR cc_start: 0.6279 (m-80) cc_final: 0.5813 (m-80) REVERT: I 97 ARG cc_start: 0.5150 (ttt-90) cc_final: 0.4816 (ttt-90) REVERT: I 99 ASP cc_start: 0.4684 (p0) cc_final: 0.4188 (p0) REVERT: M 49 LEU cc_start: 0.6592 (mp) cc_final: 0.5816 (tt) REVERT: M 94 TYR cc_start: 0.8411 (t80) cc_final: 0.8183 (t80) outliers start: 42 outliers final: 18 residues processed: 188 average time/residue: 0.1727 time to fit residues: 53.3626 Evaluate side-chains 171 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 12 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 88 optimal weight: 0.3980 chunk 172 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 101 optimal weight: 0.0670 chunk 330 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 30.0000 chunk 36 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.153202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.098641 restraints weight = 44911.419| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 4.22 r_work: 0.3218 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27730 Z= 0.121 Angle : 0.648 16.600 37996 Z= 0.300 Chirality : 0.050 0.528 4665 Planarity : 0.004 0.043 4695 Dihedral : 4.388 20.976 3596 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.69 % Allowed : 12.21 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3325 helix: 2.23 (0.20), residues: 683 sheet: 0.05 (0.17), residues: 903 loop : -1.13 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 102 TYR 0.023 0.001 TYR M 94 PHE 0.021 0.001 PHE C 559 TRP 0.028 0.001 TRP H 47 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (27583) covalent geometry : angle 0.59892 / 0.29 (37597) SS BOND : bond 0.00255 / 0.19 ( 42) SS BOND : angle 0.85313 / 0.50 ( 84) hydrogen bonds : bond 0.04174 / 2.70 ( 1090) hydrogen bonds : angle 5.24237 / 3.74 ( 3036) link_ALPHA1-6 : bond 0.00474 / 0.21 ( 3) link_ALPHA1-6 : angle 1.36864 / 0.77 ( 9) link_BETA1-4 : bond 0.01028 / 0.68 ( 55) link_BETA1-4 : angle 2.36898 / 1.72 ( 165) link_BETA1-6 : bond 0.00484 / 0.21 ( 3) link_BETA1-6 : angle 1.15938 / 0.66 ( 9) link_NAG-ASN : bond 0.00619 / 0.38 ( 44) link_NAG-ASN : angle 3.32413 / 2.06 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7287 (m-80) cc_final: 0.6390 (m-80) REVERT: A 241 LEU cc_start: 0.7257 (tt) cc_final: 0.6879 (pp) REVERT: A 697 MET cc_start: 0.8992 (ptm) cc_final: 0.8748 (ptp) REVERT: A 1107 ARG cc_start: 0.8655 (mtt180) cc_final: 0.8123 (mtt180) REVERT: B 408 ARG cc_start: 0.8715 (tmm160) cc_final: 0.8377 (tmm160) REVERT: B 990 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: C 214 ARG cc_start: 0.8004 (mmm160) cc_final: 0.7644 (mmm160) REVERT: C 408 ARG cc_start: 0.8350 (ttp80) cc_final: 0.8075 (ttp80) REVERT: C 869 MET cc_start: 0.8575 (mtt) cc_final: 0.8370 (mtt) REVERT: C 984 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8131 (tt) REVERT: C 1050 MET cc_start: 0.8847 (ptm) cc_final: 0.8635 (ptm) REVERT: H 16 GLN cc_start: 0.4854 (OUTLIER) cc_final: 0.4379 (pm20) REVERT: H 36 TRP cc_start: 0.5356 (m100) cc_final: 0.4850 (m100) REVERT: H 77 GLN cc_start: 0.8944 (pt0) cc_final: 0.8599 (pm20) REVERT: H 80 LEU cc_start: 0.7761 (tt) cc_final: 0.7491 (tp) REVERT: I 32 TYR cc_start: 0.5855 (m-80) cc_final: 0.5196 (m-80) REVERT: I 99 ASP cc_start: 0.4500 (p0) cc_final: 0.4281 (p0) REVERT: L 36 ASN cc_start: 0.7509 (t0) cc_final: 0.6923 (m-40) REVERT: L 50 ILE cc_start: 0.7214 (mt) cc_final: 0.6280 (mt) REVERT: M 49 LEU cc_start: 0.6493 (mp) cc_final: 0.5903 (tp) REVERT: M 94 TYR cc_start: 0.8388 (t80) cc_final: 0.8155 (t80) outliers start: 46 outliers final: 17 residues processed: 207 average time/residue: 0.1760 time to fit residues: 59.5302 Evaluate side-chains 178 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain M residue 53 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 326 optimal weight: 20.0000 chunk 173 optimal weight: 0.9990 chunk 333 optimal weight: 40.0000 chunk 304 optimal weight: 6.9990 chunk 266 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 299 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 268 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 955 ASN C 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.150543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.094368 restraints weight = 45165.871| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.93 r_work: 0.3152 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 27730 Z= 0.216 Angle : 0.685 16.521 37996 Z= 0.321 Chirality : 0.051 0.518 4665 Planarity : 0.004 0.046 4695 Dihedral : 4.459 19.326 3596 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.54 % Allowed : 13.16 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3325 helix: 2.11 (0.20), residues: 683 sheet: 0.04 (0.17), residues: 925 loop : -1.16 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.021 0.002 TYR B1067 PHE 0.036 0.002 PHE C 559 TRP 0.026 0.002 TRP H 47 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (27583) covalent geometry : angle 0.63865 / 0.31 (37597) SS BOND : bond 0.00338 / 0.25 ( 42) SS BOND : angle 1.01074 / 0.61 ( 84) hydrogen bonds : bond 0.04840 / 3.14 ( 1090) hydrogen bonds : angle 5.30917 / 3.80 ( 3036) link_ALPHA1-6 : bond 0.00367 / 0.16 ( 3) link_ALPHA1-6 : angle 1.46003 / 0.81 ( 9) link_BETA1-4 : bond 0.01007 / 0.67 ( 55) link_BETA1-4 : angle 2.34014 / 1.70 ( 165) link_BETA1-6 : bond 0.00404 / 0.17 ( 3) link_BETA1-6 : angle 1.24804 / 0.70 ( 9) link_NAG-ASN : bond 0.00547 / 0.34 ( 44) link_NAG-ASN : angle 3.36453 / 2.09 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7547 (m-80) cc_final: 0.6629 (m-80) REVERT: A 241 LEU cc_start: 0.7343 (tt) cc_final: 0.6959 (pp) REVERT: A 697 MET cc_start: 0.9021 (ptm) cc_final: 0.8771 (ptp) REVERT: A 1107 ARG cc_start: 0.8652 (mtt180) cc_final: 0.8303 (mtt180) REVERT: B 200 TYR cc_start: 0.7972 (m-80) cc_final: 0.7731 (m-80) REVERT: B 214 ARG cc_start: 0.8635 (mmm160) cc_final: 0.8434 (mmm160) REVERT: B 408 ARG cc_start: 0.8673 (tmm160) cc_final: 0.8326 (tmm160) REVERT: B 990 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: C 408 ARG cc_start: 0.8396 (ttp80) cc_final: 0.8106 (ttp80) REVERT: C 869 MET cc_start: 0.8639 (mtt) cc_final: 0.8417 (mtt) REVERT: C 984 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8121 (tt) REVERT: C 1050 MET cc_start: 0.8819 (ptm) cc_final: 0.8605 (ptm) REVERT: H 16 GLN cc_start: 0.5103 (OUTLIER) cc_final: 0.4586 (pm20) REVERT: H 36 TRP cc_start: 0.5413 (m100) cc_final: 0.4788 (m100) REVERT: H 77 GLN cc_start: 0.8991 (pt0) cc_final: 0.8641 (pm20) REVERT: H 80 LEU cc_start: 0.7695 (tt) cc_final: 0.7490 (tp) REVERT: M 49 LEU cc_start: 0.6616 (mp) cc_final: 0.5901 (tt) REVERT: M 94 TYR cc_start: 0.8399 (t80) cc_final: 0.8157 (t80) outliers start: 42 outliers final: 26 residues processed: 194 average time/residue: 0.1710 time to fit residues: 55.1144 Evaluate side-chains 185 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 262 optimal weight: 0.3980 chunk 138 optimal weight: 9.9990 chunk 332 optimal weight: 40.0000 chunk 76 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 109 optimal weight: 0.0570 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.153424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.099502 restraints weight = 44679.357| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 4.21 r_work: 0.3210 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 27730 Z= 0.120 Angle : 0.636 16.638 37996 Z= 0.293 Chirality : 0.049 0.495 4665 Planarity : 0.004 0.045 4695 Dihedral : 4.220 18.664 3596 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.58 % Allowed : 13.68 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.14), residues: 3325 helix: 2.35 (0.20), residues: 681 sheet: 0.09 (0.17), residues: 908 loop : -1.07 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.017 0.001 TYR B 453 PHE 0.022 0.001 PHE C 562 TRP 0.029 0.001 TRP H 47 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (27583) covalent geometry : angle 0.58764 / 0.28 (37597) SS BOND : bond 0.00274 / 0.21 ( 42) SS BOND : angle 1.13802 / 0.53 ( 84) hydrogen bonds : bond 0.03983 / 2.58 ( 1090) hydrogen bonds : angle 5.09827 / 3.64 ( 3036) link_ALPHA1-6 : bond 0.00461 / 0.21 ( 3) link_ALPHA1-6 : angle 1.37613 / 0.77 ( 9) link_BETA1-4 : bond 0.01030 / 0.68 ( 55) link_BETA1-4 : angle 2.34670 / 1.71 ( 165) link_BETA1-6 : bond 0.00444 / 0.19 ( 3) link_BETA1-6 : angle 1.16863 / 0.66 ( 9) link_NAG-ASN : bond 0.00590 / 0.37 ( 44) link_NAG-ASN : angle 3.20176 / 1.98 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 1.186 Fit side-chains REVERT: A 133 PHE cc_start: 0.7434 (m-80) cc_final: 0.6400 (m-80) REVERT: A 241 LEU cc_start: 0.7243 (tt) cc_final: 0.6834 (pp) REVERT: A 740 MET cc_start: 0.8909 (tpt) cc_final: 0.8388 (tpt) REVERT: A 1107 ARG cc_start: 0.8649 (mtt180) cc_final: 0.8245 (mtp85) REVERT: B 200 TYR cc_start: 0.7912 (m-80) cc_final: 0.7501 (m-80) REVERT: B 408 ARG cc_start: 0.8701 (tmm160) cc_final: 0.8459 (tmm160) REVERT: B 752 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8860 (mp) REVERT: B 990 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: C 298 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8215 (tp30) REVERT: C 346 ARG cc_start: 0.7550 (mmm160) cc_final: 0.7144 (mmm160) REVERT: C 408 ARG cc_start: 0.8490 (ttp80) cc_final: 0.8215 (ttp80) REVERT: C 984 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8147 (tt) REVERT: C 1050 MET cc_start: 0.8807 (ptm) cc_final: 0.8602 (ptm) REVERT: H 16 GLN cc_start: 0.5149 (OUTLIER) cc_final: 0.4615 (pm20) REVERT: H 36 TRP cc_start: 0.5448 (m100) cc_final: 0.4869 (m100) REVERT: H 77 GLN cc_start: 0.8964 (pt0) cc_final: 0.8626 (pm20) REVERT: H 80 LEU cc_start: 0.7681 (tt) cc_final: 0.7463 (tp) REVERT: M 49 LEU cc_start: 0.6535 (mp) cc_final: 0.5866 (tt) REVERT: M 94 TYR cc_start: 0.8386 (t80) cc_final: 0.8152 (t80) outliers start: 43 outliers final: 25 residues processed: 202 average time/residue: 0.1684 time to fit residues: 55.9962 Evaluate side-chains 192 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain M residue 53 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 127 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 308 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 321 optimal weight: 8.9990 chunk 132 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.151800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.095800 restraints weight = 45181.057| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 4.03 r_work: 0.3173 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27730 Z= 0.173 Angle : 0.656 16.486 37996 Z= 0.304 Chirality : 0.050 0.484 4665 Planarity : 0.004 0.046 4695 Dihedral : 4.239 18.555 3596 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.50 % Allowed : 14.19 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.14), residues: 3325 helix: 2.26 (0.20), residues: 684 sheet: 0.05 (0.17), residues: 912 loop : -1.09 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 214 TYR 0.020 0.001 TYR B1067 PHE 0.029 0.001 PHE C 559 TRP 0.029 0.001 TRP H 47 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (27583) covalent geometry : angle 0.60797 / 0.29 (37597) SS BOND : bond 0.00290 / 0.22 ( 42) SS BOND : angle 1.32027 / 0.65 ( 84) hydrogen bonds : bond 0.04406 / 2.85 ( 1090) hydrogen bonds : angle 5.10965 / 3.65 ( 3036) link_ALPHA1-6 : bond 0.00388 / 0.17 ( 3) link_ALPHA1-6 : angle 1.43596 / 0.79 ( 9) link_BETA1-4 : bond 0.00999 / 0.66 ( 55) link_BETA1-4 : angle 2.32576 / 1.69 ( 165) link_BETA1-6 : bond 0.00390 / 0.17 ( 3) link_BETA1-6 : angle 1.23521 / 0.70 ( 9) link_NAG-ASN : bond 0.00536 / 0.33 ( 44) link_NAG-ASN : angle 3.21086 / 1.98 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7377 (m-80) cc_final: 0.6392 (m-80) REVERT: A 241 LEU cc_start: 0.7475 (tt) cc_final: 0.7080 (pp) REVERT: A 740 MET cc_start: 0.8910 (tpt) cc_final: 0.8438 (tpt) REVERT: A 1107 ARG cc_start: 0.8643 (mtt180) cc_final: 0.8317 (mtt180) REVERT: B 200 TYR cc_start: 0.8007 (m-80) cc_final: 0.7603 (m-80) REVERT: B 408 ARG cc_start: 0.8690 (tmm160) cc_final: 0.8447 (tmm160) REVERT: B 752 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8842 (mp) REVERT: B 990 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: C 346 ARG cc_start: 0.7511 (mmm160) cc_final: 0.7234 (mmm160) REVERT: C 408 ARG cc_start: 0.8494 (ttp80) cc_final: 0.8207 (ttp80) REVERT: C 984 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8141 (tt) REVERT: C 1050 MET cc_start: 0.8810 (ptm) cc_final: 0.8597 (ptm) REVERT: H 16 GLN cc_start: 0.5144 (OUTLIER) cc_final: 0.4613 (pm20) REVERT: H 36 TRP cc_start: 0.5355 (m100) cc_final: 0.4842 (m100) REVERT: H 77 GLN cc_start: 0.8982 (pt0) cc_final: 0.8669 (pm20) REVERT: I 107 MET cc_start: 0.5364 (tpp) cc_final: 0.4268 (tpp) REVERT: M 49 LEU cc_start: 0.6460 (mp) cc_final: 0.5760 (tt) REVERT: M 94 TYR cc_start: 0.8460 (t80) cc_final: 0.8213 (t80) outliers start: 41 outliers final: 30 residues processed: 186 average time/residue: 0.1811 time to fit residues: 55.2458 Evaluate side-chains 189 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain M residue 53 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 219 optimal weight: 7.9990 chunk 26 optimal weight: 40.0000 chunk 307 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 262 optimal weight: 0.0270 chunk 167 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 overall best weight: 1.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.152396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.098150 restraints weight = 44771.873| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 4.24 r_work: 0.3189 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27730 Z= 0.147 Angle : 0.639 16.548 37996 Z= 0.295 Chirality : 0.049 0.474 4665 Planarity : 0.004 0.045 4695 Dihedral : 4.166 18.228 3596 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.72 % Allowed : 14.26 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.14), residues: 3325 helix: 2.42 (0.20), residues: 669 sheet: 0.05 (0.17), residues: 912 loop : -1.05 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 214 TYR 0.019 0.001 TYR B1067 PHE 0.026 0.001 PHE C 562 TRP 0.031 0.001 TRP H 47 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (27583) covalent geometry : angle 0.59220 / 0.28 (37597) SS BOND : bond 0.00259 / 0.20 ( 42) SS BOND : angle 1.07902 / 0.56 ( 84) hydrogen bonds : bond 0.04194 / 2.72 ( 1090) hydrogen bonds : angle 5.02392 / 3.58 ( 3036) link_ALPHA1-6 : bond 0.00418 / 0.19 ( 3) link_ALPHA1-6 : angle 1.40828 / 0.78 ( 9) link_BETA1-4 : bond 0.01004 / 0.66 ( 55) link_BETA1-4 : angle 2.32396 / 1.69 ( 165) link_BETA1-6 : bond 0.00390 / 0.16 ( 3) link_BETA1-6 : angle 1.20742 / 0.68 ( 9) link_NAG-ASN : bond 0.00539 / 0.34 ( 44) link_NAG-ASN : angle 3.13384 / 1.93 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.978 Fit side-chains REVERT: A 133 PHE cc_start: 0.7243 (m-80) cc_final: 0.6225 (m-80) REVERT: A 241 LEU cc_start: 0.7481 (tt) cc_final: 0.7144 (pp) REVERT: A 1107 ARG cc_start: 0.8629 (mtt180) cc_final: 0.8291 (mtt180) REVERT: B 200 TYR cc_start: 0.7978 (m-80) cc_final: 0.7616 (m-80) REVERT: B 408 ARG cc_start: 0.8711 (tmm160) cc_final: 0.8455 (tmm160) REVERT: B 752 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8859 (mp) REVERT: B 990 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: C 346 ARG cc_start: 0.7554 (mmm160) cc_final: 0.7272 (mmm160) REVERT: C 408 ARG cc_start: 0.8487 (ttp80) cc_final: 0.8216 (ttp80) REVERT: C 984 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8217 (tt) REVERT: C 1050 MET cc_start: 0.8796 (ptm) cc_final: 0.8582 (ptm) REVERT: H 16 GLN cc_start: 0.5233 (OUTLIER) cc_final: 0.4744 (pm20) REVERT: H 36 TRP cc_start: 0.5370 (m100) cc_final: 0.4720 (m100) REVERT: H 77 GLN cc_start: 0.8976 (pt0) cc_final: 0.8637 (pm20) REVERT: I 107 MET cc_start: 0.5149 (tpp) cc_final: 0.3893 (tpp) REVERT: M 49 LEU cc_start: 0.6467 (mp) cc_final: 0.5760 (tt) REVERT: M 94 TYR cc_start: 0.8528 (t80) cc_final: 0.8285 (t80) outliers start: 47 outliers final: 32 residues processed: 197 average time/residue: 0.1705 time to fit residues: 55.4862 Evaluate side-chains 192 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 92 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 250 optimal weight: 4.9990 chunk 277 optimal weight: 1.9990 chunk 171 optimal weight: 0.0870 chunk 39 optimal weight: 7.9990 chunk 189 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 137 optimal weight: 8.9990 chunk 222 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 255 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.154185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.098053 restraints weight = 44765.682| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.22 r_work: 0.3255 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27730 Z= 0.114 Angle : 0.622 16.584 37996 Z= 0.285 Chirality : 0.049 0.454 4665 Planarity : 0.004 0.046 4695 Dihedral : 4.009 17.326 3596 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.36 % Allowed : 14.81 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3325 helix: 2.59 (0.20), residues: 667 sheet: 0.17 (0.17), residues: 902 loop : -1.00 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 92 TYR 0.017 0.001 TYR B1067 PHE 0.018 0.001 PHE A 592 TRP 0.033 0.001 TRP H 47 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (27583) covalent geometry : angle 0.57650 / 0.27 (37597) SS BOND : bond 0.00204 / 0.15 ( 42) SS BOND : angle 0.87583 / 0.48 ( 84) hydrogen bonds : bond 0.03736 / 2.41 ( 1090) hydrogen bonds : angle 4.90411 / 3.49 ( 3036) link_ALPHA1-6 : bond 0.00431 / 0.20 ( 3) link_ALPHA1-6 : angle 1.38593 / 0.76 ( 9) link_BETA1-4 : bond 0.01027 / 0.68 ( 55) link_BETA1-4 : angle 2.32737 / 1.69 ( 165) link_BETA1-6 : bond 0.00408 / 0.18 ( 3) link_BETA1-6 : angle 1.19441 / 0.68 ( 9) link_NAG-ASN : bond 0.00563 / 0.36 ( 44) link_NAG-ASN : angle 3.02746 / 1.86 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7339 (m-80) cc_final: 0.6257 (m-80) REVERT: A 241 LEU cc_start: 0.7457 (tt) cc_final: 0.7237 (pp) REVERT: A 1107 ARG cc_start: 0.8592 (mtt180) cc_final: 0.8336 (mtt180) REVERT: B 200 TYR cc_start: 0.7914 (m-80) cc_final: 0.7556 (m-80) REVERT: B 408 ARG cc_start: 0.8708 (tmm160) cc_final: 0.8447 (tmm160) REVERT: B 752 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8877 (mp) REVERT: B 990 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: C 346 ARG cc_start: 0.7540 (mmm160) cc_final: 0.7266 (mmm160) REVERT: C 408 ARG cc_start: 0.8481 (ttp80) cc_final: 0.8214 (ttp80) REVERT: C 984 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8131 (tt) REVERT: C 1050 MET cc_start: 0.8758 (ptm) cc_final: 0.8546 (ptm) REVERT: H 16 GLN cc_start: 0.5310 (OUTLIER) cc_final: 0.4769 (pm20) REVERT: H 36 TRP cc_start: 0.5309 (m100) cc_final: 0.4638 (m100) REVERT: H 77 GLN cc_start: 0.8993 (pt0) cc_final: 0.8589 (pm20) REVERT: I 39 GLN cc_start: 0.5707 (tm-30) cc_final: 0.5401 (pp30) REVERT: I 107 MET cc_start: 0.5547 (tpp) cc_final: 0.4327 (tpp) REVERT: L 12 THR cc_start: 0.6034 (OUTLIER) cc_final: 0.5786 (m) REVERT: L 34 TYR cc_start: 0.5465 (t80) cc_final: 0.5237 (t80) REVERT: L 36 ASN cc_start: 0.8128 (t0) cc_final: 0.6961 (m110) REVERT: L 38 VAL cc_start: 0.4509 (m) cc_final: 0.3906 (t) REVERT: M 49 LEU cc_start: 0.6494 (mp) cc_final: 0.5748 (tt) REVERT: M 94 TYR cc_start: 0.8571 (t80) cc_final: 0.8353 (t80) outliers start: 37 outliers final: 26 residues processed: 198 average time/residue: 0.1703 time to fit residues: 55.5955 Evaluate side-chains 193 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 92 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 152 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 33 optimal weight: 40.0000 chunk 154 optimal weight: 0.5980 chunk 208 optimal weight: 0.9990 chunk 289 optimal weight: 0.0570 chunk 181 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 264 optimal weight: 0.0470 chunk 97 optimal weight: 0.9980 chunk 138 optimal weight: 0.1980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 762 GLN H 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.155167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.099555 restraints weight = 44503.331| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.22 r_work: 0.3275 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 27730 Z= 0.108 Angle : 0.619 16.587 37996 Z= 0.285 Chirality : 0.048 0.446 4665 Planarity : 0.004 0.045 4695 Dihedral : 3.916 17.060 3596 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.25 % Allowed : 15.18 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.14), residues: 3325 helix: 2.57 (0.20), residues: 669 sheet: 0.21 (0.17), residues: 894 loop : -0.95 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 92 TYR 0.018 0.001 TYR A 170 PHE 0.034 0.001 PHE C 562 TRP 0.034 0.001 TRP H 47 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (27583) covalent geometry : angle 0.57345 / 0.27 (37597) SS BOND : bond 0.00194 / 0.15 ( 42) SS BOND : angle 1.15662 / 0.68 ( 84) hydrogen bonds : bond 0.03618 / 2.29 ( 1090) hydrogen bonds : angle 4.84269 / 3.43 ( 3036) link_ALPHA1-6 : bond 0.00446 / 0.20 ( 3) link_ALPHA1-6 : angle 1.38438 / 0.76 ( 9) link_BETA1-4 : bond 0.01010 / 0.67 ( 55) link_BETA1-4 : angle 2.31892 / 1.69 ( 165) link_BETA1-6 : bond 0.00389 / 0.17 ( 3) link_BETA1-6 : angle 1.19903 / 0.68 ( 9) link_NAG-ASN : bond 0.00569 / 0.36 ( 44) link_NAG-ASN : angle 2.96713 / 1.82 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6986.69 seconds wall clock time: 120 minutes 32.37 seconds (7232.37 seconds total)