Starting phenix.real_space_refine on Fri Sep 19 07:21:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9db0_46709/09_2025/9db0_46709.cif Found real_map, /net/cci-nas-00/data/ceres_data/9db0_46709/09_2025/9db0_46709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9db0_46709/09_2025/9db0_46709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9db0_46709/09_2025/9db0_46709.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9db0_46709/09_2025/9db0_46709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9db0_46709/09_2025/9db0_46709.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.064 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 120 5.16 5 C 15231 2.51 5 N 3807 2.21 5 O 4854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24012 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 7382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7382 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 35, 'TRANS': 960} Chain breaks: 5 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ASP:plan': 20, 'GLU:plan': 14, 'GLN:plan1': 5, 'ASN:plan1': 6, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 179 Chain: "B" Number of atoms: 7382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7382 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 35, 'TRANS': 960} Chain breaks: 5 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ASP:plan': 20, 'GLU:plan': 14, 'GLN:plan1': 5, 'ASN:plan1': 6, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 179 Chain: "C" Number of atoms: 7382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7382 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 35, 'TRANS': 960} Chain breaks: 5 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ASP:plan': 20, 'GLU:plan': 14, 'GLN:plan1': 5, 'ASN:plan1': 6, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 179 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 134 Unusual residues: {'NAG': 7, 'PAM': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 134 Unusual residues: {'NAG': 7, 'PAM': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 134 Unusual residues: {'NAG': 7, 'PAM': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Time building chain proxies: 6.08, per 1000 atoms: 0.25 Number of scatterers: 24012 At special positions: 0 Unit cell: (135, 131, 159, 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 120 16.00 O 4854 8.00 N 3807 7.00 C 15231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 333 " distance=2.05 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 450 " distance=2.18 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 405 " distance=2.05 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 498 " distance=2.03 Simple disulfide: pdb=" SG CYS A 573 " - pdb=" SG CYS A 632 " distance=2.03 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 600 " distance=2.03 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 642 " distance=2.03 Simple disulfide: pdb=" SG CYS A 691 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 803 " - pdb=" SG CYS A 815 " distance=2.03 Simple disulfide: pdb=" SG CYS A 866 " - pdb=" SG CYS A 888 " distance=2.03 Simple disulfide: pdb=" SG CYS A 871 " - pdb=" SG CYS A 877 " distance=2.03 Simple disulfide: pdb=" SG CYS A 989 " - pdb=" SG CYS A1000 " distance=2.03 Simple disulfide: pdb=" SG CYS A1192 " - pdb=" SG CYS A1203 " distance=2.03 Simple disulfide: pdb=" SG CYS A1242 " - pdb=" SG CYS A1293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 333 " distance=2.06 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 450 " distance=2.18 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 405 " distance=2.05 Simple disulfide: pdb=" SG CYS B 489 " - pdb=" SG CYS B 498 " distance=2.03 Simple disulfide: pdb=" SG CYS B 573 " - pdb=" SG CYS B 632 " distance=2.03 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 600 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 642 " distance=2.03 Simple disulfide: pdb=" SG CYS B 691 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 803 " - pdb=" SG CYS B 815 " distance=2.03 Simple disulfide: pdb=" SG CYS B 866 " - pdb=" SG CYS B 888 " distance=2.03 Simple disulfide: pdb=" SG CYS B 871 " - pdb=" SG CYS B 877 " distance=2.03 Simple disulfide: pdb=" SG CYS B 989 " - pdb=" SG CYS B1000 " distance=2.03 Simple disulfide: pdb=" SG CYS B1192 " - pdb=" SG CYS B1203 " distance=2.03 Simple disulfide: pdb=" SG CYS B1242 " - pdb=" SG CYS B1293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 333 " distance=2.05 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 450 " distance=2.18 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 405 " distance=2.05 Simple disulfide: pdb=" SG CYS C 489 " - pdb=" SG CYS C 498 " distance=2.03 Simple disulfide: pdb=" SG CYS C 573 " - pdb=" SG CYS C 632 " distance=2.03 Simple disulfide: pdb=" SG CYS C 587 " - pdb=" SG CYS C 600 " distance=2.03 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 642 " distance=2.03 Simple disulfide: pdb=" SG CYS C 691 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 803 " - pdb=" SG CYS C 815 " distance=2.03 Simple disulfide: pdb=" SG CYS C 866 " - pdb=" SG CYS C 888 " distance=2.03 Simple disulfide: pdb=" SG CYS C 871 " - pdb=" SG CYS C 877 " distance=2.03 Simple disulfide: pdb=" SG CYS C 989 " - pdb=" SG CYS C1000 " distance=2.03 Simple disulfide: pdb=" SG CYS C1192 " - pdb=" SG CYS C1203 " distance=2.03 Simple disulfide: pdb=" SG CYS C1242 " - pdb=" SG CYS C1293 " 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 ALPHA1-3 " BMA L 3 " - " MAN L 4 " " BMA N 3 " - " MAN N 4 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 4 " " BMA l 3 " - " MAN l 4 " " BMA n 3 " - " MAN n 4 " ALPHA1-6 " BMA L 3 " - " MAN L 5 " " BMA Y 3 " - " MAN Y 5 " " BMA l 3 " - " MAN l 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A1501 " - " ASN A 567 " " NAG A1502 " - " ASN A 537 " " NAG A1503 " - " ASN A 410 " " NAG A1504 " - " ASN A 785 " " NAG A1505 " - " ASN A 521 " " NAG A1506 " - " ASN A 380 " " NAG A1508 " - " ASN A 709 " " NAG B1502 " - " ASN B 567 " " NAG B1503 " - " ASN B 537 " " NAG B1504 " - " ASN B 410 " " NAG B1505 " - " ASN B 785 " " NAG B1506 " - " ASN B 521 " " NAG B1507 " - " ASN B 380 " " NAG B1509 " - " ASN B 709 " " NAG C1502 " - " ASN C 567 " " NAG C1503 " - " ASN C 537 " " NAG C1504 " - " ASN C 410 " " NAG C1505 " - " ASN C 785 " " NAG C1506 " - " ASN C 521 " " NAG C1507 " - " ASN C 380 " " NAG C1509 " - " ASN C 709 " " NAG D 1 " - " ASN A1299 " " NAG E 1 " - " ASN A 845 " " NAG F 1 " - " ASN A 350 " " NAG G 1 " - " ASN A 559 " " NAG H 1 " - " ASN A 730 " " NAG I 1 " - " ASN A 824 " " NAG J 1 " - " ASN A 926 " " NAG K 1 " - " ASN A1079 " " NAG L 1 " - " ASN A1205 " " NAG M 1 " - " ASN A 367 " " NAG N 1 " - " ASN A 290 " " NAG O 1 " - " ASN A 454 " " NAG P 1 " - " ASN A 839 " " NAG Q 1 " - " ASN B1299 " " NAG R 1 " - " ASN B 845 " " NAG S 1 " - " ASN B 350 " " NAG T 1 " - " ASN B 559 " " NAG U 1 " - " ASN B 730 " " NAG V 1 " - " ASN B 824 " " NAG W 1 " - " ASN B 926 " " NAG X 1 " - " ASN B1079 " " NAG Y 1 " - " ASN B1205 " " NAG Z 1 " - " ASN B 367 " " NAG a 1 " - " ASN B 290 " " NAG b 1 " - " ASN B 454 " " NAG c 1 " - " ASN B 839 " " NAG d 1 " - " ASN C1299 " " NAG e 1 " - " ASN C 845 " " NAG f 1 " - " ASN C 350 " " NAG g 1 " - " ASN C 559 " " NAG h 1 " - " ASN C 730 " " NAG i 1 " - " ASN C 824 " " NAG j 1 " - " ASN C 926 " " NAG k 1 " - " ASN C1079 " " NAG l 1 " - " ASN C1205 " " NAG m 1 " - " ASN C 367 " " NAG n 1 " - " ASN C 290 " " NAG o 1 " - " ASN C 454 " " NAG p 1 " - " ASN C 839 " Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 954.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5568 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 42 sheets defined 25.0% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 491 through 500 Processing helix chain 'A' and resid 618 through 622 Processing helix chain 'A' and resid 865 through 871 Processing helix chain 'A' and resid 874 through 882 Processing helix chain 'A' and resid 884 through 908 removed outlier: 3.538A pdb=" N CYS A 888 " --> pdb=" O TYR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 920 removed outlier: 3.517A pdb=" N LEU A 919 " --> pdb=" O ASN A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 926 Processing helix chain 'A' and resid 932 through 936 removed outlier: 3.571A pdb=" N LYS A 936 " --> pdb=" O PRO A 933 " (cutoff:3.500A) 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 950 Processing helix chain 'A' and resid 964 through 974 removed outlier: 3.508A pdb=" N VAL A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1005 Processing helix chain 'A' and resid 1012 through 1029 Processing helix chain 'A' and resid 1030 through 1032 No H-bonds generated for 'chain 'A' and resid 1030 through 1032' Processing helix chain 'A' and resid 1043 through 1056 Processing helix chain 'A' and resid 1065 through 1085 removed outlier: 4.435A pdb=" N LEU A1069 " --> pdb=" O ASN A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1125 removed outlier: 3.723A pdb=" N LEU A1119 " --> pdb=" O GLN A1115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A1122 " --> pdb=" O ALA A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1128 No H-bonds generated for 'chain 'A' and resid 1126 through 1128' Processing helix chain 'A' and resid 1136 through 1142 Processing helix chain 'A' and resid 1145 through 1193 removed outlier: 4.100A pdb=" N ALA A1151 " --> pdb=" O PRO A1147 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A1152 " --> pdb=" O SER A1148 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A1155 " --> pdb=" O ALA A1151 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A1156 " --> pdb=" O GLN A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1285 No H-bonds generated for 'chain 'A' and resid 1283 through 1285' Processing helix chain 'B' and resid 491 through 500 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 865 through 871 Processing helix chain 'B' and resid 874 through 882 Processing helix chain 'B' and resid 884 through 908 removed outlier: 3.538A pdb=" N CYS B 888 " --> pdb=" O TYR B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 920 removed outlier: 3.517A pdb=" N LEU B 919 " --> pdb=" O ASN B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 926 Processing helix chain 'B' and resid 932 through 936 removed outlier: 3.570A pdb=" N LYS B 936 " --> pdb=" O PRO B 933 " (cutoff:3.500A) 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 950 Processing helix chain 'B' and resid 964 through 974 removed outlier: 3.508A pdb=" N VAL B 974 " --> pdb=" O LEU B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1005 Processing helix chain 'B' and resid 1012 through 1029 Processing helix chain 'B' and resid 1030 through 1032 No H-bonds generated for 'chain 'B' and resid 1030 through 1032' Processing helix chain 'B' and resid 1043 through 1056 Processing helix chain 'B' and resid 1065 through 1085 removed outlier: 4.435A pdb=" N LEU B1069 " --> pdb=" O ASN B1065 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1125 removed outlier: 3.724A pdb=" N LEU B1119 " --> pdb=" O GLN B1115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B1122 " --> pdb=" O ALA B1118 " (cutoff:3.500A) Processing helix chain 'B' and resid 1126 through 1128 No H-bonds generated for 'chain 'B' and resid 1126 through 1128' Processing helix chain 'B' and resid 1136 through 1142 Processing helix chain 'B' and resid 1145 through 1193 removed outlier: 4.100A pdb=" N ALA B1151 " --> pdb=" O PRO B1147 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN B1152 " --> pdb=" O SER B1148 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG B1155 " --> pdb=" O ALA B1151 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B1156 " --> pdb=" O GLN B1152 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1285 No H-bonds generated for 'chain 'B' and resid 1283 through 1285' Processing helix chain 'C' and resid 491 through 500 Processing helix chain 'C' and resid 618 through 622 Processing helix chain 'C' and resid 865 through 871 Processing helix chain 'C' and resid 874 through 882 Processing helix chain 'C' and resid 884 through 908 removed outlier: 3.538A pdb=" N CYS C 888 " --> pdb=" O TYR C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 920 removed outlier: 3.517A pdb=" N LEU C 919 " --> pdb=" O ASN C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 926 Processing helix chain 'C' and resid 932 through 936 removed outlier: 3.570A pdb=" N LYS C 936 " --> pdb=" O PRO C 933 " (cutoff:3.500A) 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 950 Processing helix chain 'C' and resid 964 through 974 removed outlier: 3.509A pdb=" N VAL C 974 " --> pdb=" O LEU C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1005 Processing helix chain 'C' and resid 1012 through 1029 Processing helix chain 'C' and resid 1030 through 1032 No H-bonds generated for 'chain 'C' and resid 1030 through 1032' Processing helix chain 'C' and resid 1043 through 1056 Processing helix chain 'C' and resid 1065 through 1085 removed outlier: 4.435A pdb=" N LEU C1069 " --> pdb=" O ASN C1065 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1125 removed outlier: 3.723A pdb=" N LEU C1119 " --> pdb=" O GLN C1115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C1122 " --> pdb=" O ALA C1118 " (cutoff:3.500A) Processing helix chain 'C' and resid 1126 through 1128 No H-bonds generated for 'chain 'C' and resid 1126 through 1128' Processing helix chain 'C' and resid 1136 through 1142 Processing helix chain 'C' and resid 1145 through 1193 removed outlier: 4.100A pdb=" N ALA C1151 " --> pdb=" O PRO C1147 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN C1152 " --> pdb=" O SER C1148 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG C1155 " --> pdb=" O ALA C1151 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C1156 " --> pdb=" O GLN C1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1285 No H-bonds generated for 'chain 'C' and resid 1283 through 1285' Processing sheet with id=AA1, first strand: chain 'A' and resid 296 through 314 removed outlier: 6.252A pdb=" N SER A 470 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL A 307 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR A 468 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N CYS A 309 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE A 466 " --> pdb=" O CYS A 309 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP A 311 " --> pdb=" O TRP A 464 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP A 464 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 465 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N HIS A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N PHE A 435 " --> pdb=" O PHE A 442 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 296 through 314 removed outlier: 6.252A pdb=" N SER A 470 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL A 307 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR A 468 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N CYS A 309 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE A 466 " --> pdb=" O CYS A 309 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP A 311 " --> pdb=" O TRP A 464 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP A 464 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 485 " --> pdb=" O GLN A 477 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLU A 479 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 324 Processing sheet with id=AA4, first strand: chain 'A' and resid 318 through 324 removed outlier: 4.650A pdb=" N ASN A 454 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL A 363 " --> pdb=" O ASN A 454 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N THR A 362 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS A 378 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 364 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N CYS A 405 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N TYR A 416 " --> pdb=" O CYS A 405 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 407 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 513 removed outlier: 3.745A pdb=" N GLY A 757 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 751 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ILE A 755 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS A 771 " --> pdb=" O SER A 782 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 521 through 525 removed outlier: 6.574A pdb=" N ASN A 521 " --> pdb=" O ASP A 693 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ASN A 695 " --> pdb=" O ASN A 521 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER A 523 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU A 726 " --> pdb=" O VAL A 739 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 552 through 554 removed outlier: 10.822A pdb=" N TYR A 664 " --> pdb=" O SER A 634 " (cutoff:3.500A) removed outlier: 11.822A pdb=" N SER A 634 " --> pdb=" O TYR A 664 " (cutoff:3.500A) removed outlier: 11.516A pdb=" N GLU A 666 " --> pdb=" O CYS A 632 " (cutoff:3.500A) removed outlier: 11.819A pdb=" N CYS A 632 " --> pdb=" O GLU A 666 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N ASP A 668 " --> pdb=" O LYS A 630 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LYS A 630 " --> pdb=" O ASP A 668 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 559 through 561 removed outlier: 5.504A pdb=" N VAL A 656 " --> pdb=" O ALA A 648 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA A 648 " --> pdb=" O VAL A 656 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 805 through 809 removed outlier: 6.568A pdb=" N VAL A 814 " --> pdb=" O ILE A 806 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR A 808 " --> pdb=" O ILE A 812 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE A 812 " --> pdb=" O THR A 808 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 826 through 827 removed outlier: 6.414A pdb=" N THR A 826 " --> pdb=" O VAL B 912 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 838 through 843 removed outlier: 5.819A pdb=" N THR A1236 " --> pdb=" O ARG A1263 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG A1263 " --> pdb=" O THR A1236 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU A1261 " --> pdb=" O TRP A1238 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 846 through 856 removed outlier: 7.042A pdb=" N GLY A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA A1215 " --> pdb=" O GLY A1219 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A1221 " --> pdb=" O ALA A1213 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA A1213 " --> pdb=" O ILE A1221 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE A1223 " --> pdb=" O SER A1211 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER A1211 " --> pdb=" O PHE A1223 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR A1225 " --> pdb=" O LEU A1209 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A1207 " --> pdb=" O LEU A1227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 862 through 864 Processing sheet with id=AB5, first strand: chain 'A' and resid 911 through 912 Processing sheet with id=AB6, first strand: chain 'A' and resid 1287 through 1290 removed outlier: 5.984A pdb=" N CYS A1242 " --> pdb=" O ALA A1300 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 296 through 314 removed outlier: 6.252A pdb=" N SER B 470 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL B 307 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR B 468 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N CYS B 309 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE B 466 " --> pdb=" O CYS B 309 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP B 311 " --> pdb=" O TRP B 464 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP B 464 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 465 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS B 434 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N PHE B 435 " --> pdb=" O PHE B 442 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 296 through 314 removed outlier: 6.252A pdb=" N SER B 470 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL B 307 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR B 468 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N CYS B 309 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE B 466 " --> pdb=" O CYS B 309 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP B 311 " --> pdb=" O TRP B 464 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP B 464 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS B 485 " --> pdb=" O GLN B 477 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLU B 479 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE B 483 " --> pdb=" O GLU B 479 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 318 through 324 Processing sheet with id=AC1, first strand: chain 'B' and resid 318 through 324 removed outlier: 4.650A pdb=" N ASN B 454 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 363 " --> pdb=" O ASN B 454 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N THR B 362 " --> pdb=" O CYS B 378 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS B 378 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 364 " --> pdb=" O ILE B 376 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N CYS B 405 " --> pdb=" O TYR B 416 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N TYR B 416 " --> pdb=" O CYS B 405 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 407 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 508 through 513 removed outlier: 3.745A pdb=" N GLY B 757 " --> pdb=" O ALA B 749 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 751 " --> pdb=" O ILE B 755 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ILE B 755 " --> pdb=" O ILE B 751 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS B 771 " --> pdb=" O SER B 782 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 521 through 525 removed outlier: 6.574A pdb=" N ASN B 521 " --> pdb=" O ASP B 693 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASN B 695 " --> pdb=" O ASN B 521 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER B 523 " --> pdb=" O ASN B 695 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU B 726 " --> pdb=" O VAL B 739 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 552 through 554 removed outlier: 10.822A pdb=" N TYR B 664 " --> pdb=" O SER B 634 " (cutoff:3.500A) removed outlier: 11.822A pdb=" N SER B 634 " --> pdb=" O TYR B 664 " (cutoff:3.500A) removed outlier: 11.516A pdb=" N GLU B 666 " --> pdb=" O CYS B 632 " (cutoff:3.500A) removed outlier: 11.819A pdb=" N CYS B 632 " --> pdb=" O GLU B 666 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N ASP B 668 " --> pdb=" O LYS B 630 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LYS B 630 " --> pdb=" O ASP B 668 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 559 through 561 removed outlier: 5.503A pdb=" N VAL B 656 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA B 648 " --> pdb=" O VAL B 656 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 805 through 809 removed outlier: 6.568A pdb=" N VAL B 814 " --> pdb=" O ILE B 806 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR B 808 " --> pdb=" O ILE B 812 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE B 812 " --> pdb=" O THR B 808 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 826 through 827 removed outlier: 6.414A pdb=" N THR B 826 " --> pdb=" O VAL C 912 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 838 through 843 removed outlier: 5.819A pdb=" N THR B1236 " --> pdb=" O ARG B1263 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG B1263 " --> pdb=" O THR B1236 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU B1261 " --> pdb=" O TRP B1238 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 846 through 856 removed outlier: 7.041A pdb=" N GLY B1219 " --> pdb=" O ALA B1215 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA B1215 " --> pdb=" O GLY B1219 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE B1221 " --> pdb=" O ALA B1213 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA B1213 " --> pdb=" O ILE B1221 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE B1223 " --> pdb=" O SER B1211 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER B1211 " --> pdb=" O PHE B1223 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR B1225 " --> pdb=" O LEU B1209 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR B1207 " --> pdb=" O LEU B1227 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 862 through 864 Processing sheet with id=AD2, first strand: chain 'B' and resid 1287 through 1290 removed outlier: 5.983A pdb=" N CYS B1242 " --> pdb=" O ALA B1300 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 296 through 314 removed outlier: 6.252A pdb=" N SER C 470 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL C 307 " --> pdb=" O TYR C 468 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR C 468 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N CYS C 309 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 466 " --> pdb=" O CYS C 309 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP C 311 " --> pdb=" O TRP C 464 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP C 464 " --> pdb=" O TRP C 311 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 465 " --> pdb=" O ASN C 348 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N HIS C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N PHE C 435 " --> pdb=" O PHE C 442 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 296 through 314 removed outlier: 6.252A pdb=" N SER C 470 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL C 307 " --> pdb=" O TYR C 468 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR C 468 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N CYS C 309 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 466 " --> pdb=" O CYS C 309 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP C 311 " --> pdb=" O TRP C 464 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP C 464 " --> pdb=" O TRP C 311 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 485 " --> pdb=" O GLN C 477 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLU C 479 " --> pdb=" O ILE C 483 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 318 through 324 Processing sheet with id=AD6, first strand: chain 'C' and resid 318 through 324 removed outlier: 4.649A pdb=" N ASN C 454 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL C 363 " --> pdb=" O ASN C 454 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N THR C 362 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS C 378 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE C 364 " --> pdb=" O ILE C 376 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N CYS C 405 " --> pdb=" O TYR C 416 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N TYR C 416 " --> pdb=" O CYS C 405 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL C 407 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 508 through 513 removed outlier: 3.745A pdb=" N GLY C 757 " --> pdb=" O ALA C 749 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE C 751 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ILE C 755 " --> pdb=" O ILE C 751 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS C 771 " --> pdb=" O SER C 782 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 521 through 525 removed outlier: 6.575A pdb=" N ASN C 521 " --> pdb=" O ASP C 693 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASN C 695 " --> pdb=" O ASN C 521 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER C 523 " --> pdb=" O ASN C 695 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU C 726 " --> pdb=" O VAL C 739 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 552 through 554 removed outlier: 10.822A pdb=" N TYR C 664 " --> pdb=" O SER C 634 " (cutoff:3.500A) removed outlier: 11.822A pdb=" N SER C 634 " --> pdb=" O TYR C 664 " (cutoff:3.500A) removed outlier: 11.516A pdb=" N GLU C 666 " --> pdb=" O CYS C 632 " (cutoff:3.500A) removed outlier: 11.819A pdb=" N CYS C 632 " --> pdb=" O GLU C 666 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N ASP C 668 " --> pdb=" O LYS C 630 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LYS C 630 " --> pdb=" O ASP C 668 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 559 through 561 removed outlier: 5.503A pdb=" N VAL C 656 " --> pdb=" O ALA C 648 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA C 648 " --> pdb=" O VAL C 656 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 805 through 809 removed outlier: 6.568A pdb=" N VAL C 814 " --> pdb=" O ILE C 806 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR C 808 " --> pdb=" O ILE C 812 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE C 812 " --> pdb=" O THR C 808 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 838 through 843 removed outlier: 5.819A pdb=" N THR C1236 " --> pdb=" O ARG C1263 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG C1263 " --> pdb=" O THR C1236 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU C1261 " --> pdb=" O TRP C1238 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 846 through 856 removed outlier: 7.041A pdb=" N GLY C1219 " --> pdb=" O ALA C1215 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA C1215 " --> pdb=" O GLY C1219 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE C1221 " --> pdb=" O ALA C1213 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA C1213 " --> pdb=" O ILE C1221 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE C1223 " --> pdb=" O SER C1211 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER C1211 " --> pdb=" O PHE C1223 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR C1225 " --> pdb=" O LEU C1209 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR C1207 " --> pdb=" O LEU C1227 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 862 through 864 Processing sheet with id=AE6, first strand: chain 'C' and resid 1287 through 1290 removed outlier: 5.983A pdb=" N CYS C1242 " --> pdb=" O ALA C1300 " (cutoff:3.500A) 1018 hydrogen bonds defined for protein. 2910 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: 6.19 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3729 1.31 - 1.44: 7016 1.44 - 1.57: 13438 1.57 - 1.69: 0 1.69 - 1.82: 156 Bond restraints: 24339 Sorted by residual: bond pdb=" N PRO C 402 " pdb=" CD PRO C 402 " ideal model delta sigma weight residual 1.473 1.554 -0.081 1.40e-02 5.10e+03 3.35e+01 bond pdb=" N PRO B 402 " pdb=" CD PRO B 402 " ideal model delta sigma weight residual 1.473 1.554 -0.081 1.40e-02 5.10e+03 3.33e+01 bond pdb=" N PRO A 402 " pdb=" CD PRO A 402 " ideal model delta sigma weight residual 1.473 1.554 -0.081 1.40e-02 5.10e+03 3.31e+01 bond pdb=" CA SER C 331 " pdb=" CB SER C 331 " ideal model delta sigma weight residual 1.530 1.474 0.056 1.24e-02 6.50e+03 2.01e+01 bond pdb=" CA SER A 331 " pdb=" CB SER A 331 " ideal model delta sigma weight residual 1.530 1.475 0.055 1.24e-02 6.50e+03 2.00e+01 ... (remaining 24334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 32454 2.32 - 4.64: 687 4.64 - 6.97: 63 6.97 - 9.29: 12 9.29 - 11.61: 6 Bond angle restraints: 33222 Sorted by residual: angle pdb=" N CYS C 333 " pdb=" CA CYS C 333 " pdb=" CB CYS C 333 " ideal model delta sigma weight residual 110.84 99.23 11.61 1.52e+00 4.33e-01 5.83e+01 angle pdb=" N CYS A 333 " pdb=" CA CYS A 333 " pdb=" CB CYS A 333 " ideal model delta sigma weight residual 110.84 99.24 11.60 1.52e+00 4.33e-01 5.82e+01 angle pdb=" N CYS B 333 " pdb=" CA CYS B 333 " pdb=" CB CYS B 333 " ideal model delta sigma weight residual 110.84 99.27 11.57 1.52e+00 4.33e-01 5.79e+01 angle pdb=" N VAL A 363 " pdb=" CA VAL A 363 " pdb=" C VAL A 363 " ideal model delta sigma weight residual 112.96 106.77 6.19 1.00e+00 1.00e+00 3.83e+01 angle pdb=" N VAL B 363 " pdb=" CA VAL B 363 " pdb=" C VAL B 363 " ideal model delta sigma weight residual 112.96 106.78 6.18 1.00e+00 1.00e+00 3.82e+01 ... (remaining 33217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 15018 21.39 - 42.79: 573 42.79 - 64.18: 123 64.18 - 85.57: 81 85.57 - 106.97: 39 Dihedral angle restraints: 15834 sinusoidal: 7155 harmonic: 8679 Sorted by residual: dihedral pdb=" CD ARG A1174 " pdb=" NE ARG A1174 " pdb=" CZ ARG A1174 " pdb=" NH1 ARG A1174 " ideal model delta sinusoidal sigma weight residual 0.00 77.92 -77.92 1 1.00e+01 1.00e-02 7.59e+01 dihedral pdb=" CD ARG B1174 " pdb=" NE ARG B1174 " pdb=" CZ ARG B1174 " pdb=" NH1 ARG B1174 " ideal model delta sinusoidal sigma weight residual 0.00 77.88 -77.88 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CD ARG C1174 " pdb=" NE ARG C1174 " pdb=" CZ ARG C1174 " pdb=" NH1 ARG C1174 " ideal model delta sinusoidal sigma weight residual 0.00 77.83 -77.83 1 1.00e+01 1.00e-02 7.58e+01 ... (remaining 15831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 3785 0.086 - 0.173: 427 0.173 - 0.259: 45 0.259 - 0.345: 9 0.345 - 0.431: 9 Chirality restraints: 4275 Sorted by residual: chirality pdb=" C1 BMA n 3 " pdb=" O4 NAG n 2 " pdb=" C2 BMA n 3 " pdb=" O5 BMA n 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-02 2.50e+03 4.65e+02 chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-02 2.50e+03 4.60e+02 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-02 2.50e+03 4.58e+02 ... (remaining 4272 not shown) Planarity restraints: 4131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B1174 " 1.076 9.50e-02 1.11e+02 4.82e-01 1.40e+02 pdb=" NE ARG B1174 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B1174 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B1174 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B1174 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1174 " -1.075 9.50e-02 1.11e+02 4.82e-01 1.40e+02 pdb=" NE ARG A1174 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG A1174 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A1174 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A1174 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C1174 " -1.075 9.50e-02 1.11e+02 4.82e-01 1.40e+02 pdb=" NE ARG C1174 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG C1174 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C1174 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C1174 " -0.020 2.00e-02 2.50e+03 ... (remaining 4128 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 195 2.66 - 3.22: 20660 3.22 - 3.78: 35831 3.78 - 4.34: 52120 4.34 - 4.90: 83935 Nonbonded interactions: 192741 Sorted by model distance: nonbonded pdb=" OG1 THR B 775 " pdb=" O PHE B 778 " model vdw 2.097 3.040 nonbonded pdb=" OG1 THR A 775 " pdb=" O PHE A 778 " model vdw 2.097 3.040 nonbonded pdb=" OG1 THR C 775 " pdb=" O PHE C 778 " model vdw 2.097 3.040 nonbonded pdb=" O CYS A 989 " pdb=" OH TYR A1004 " model vdw 2.310 3.040 nonbonded pdb=" O CYS C 989 " pdb=" OH TYR C1004 " model vdw 2.310 3.040 ... (remaining 192736 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 265 through 1307 or resid 1502 through 1506)) selection = (chain 'B' and (resid 265 through 1307 or resid 1502 through 1506)) selection = (chain 'C' and (resid 265 through 1307 or resid 1502 through 1506)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'm' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'V' selection = chain 'X' selection = chain 'i' selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'Y' selection = chain 'l' } ncs_group { reference = chain 'N' selection = chain 'a' selection = chain 'n' } 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: 13.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 24.590 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.090 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:9.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.148 24501 Z= 0.355 Angle : 0.821 12.447 33666 Z= 0.482 Chirality : 0.056 0.431 4275 Planarity : 0.014 0.482 4071 Dihedral : 14.157 106.967 10140 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.32 % Favored : 98.58 % Rotamer: Outliers : 1.38 % Allowed : 6.88 % Favored : 91.74 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.15), residues: 2952 helix: 2.65 (0.20), residues: 693 sheet: 0.52 (0.18), residues: 783 loop : -0.69 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1280 TYR 0.016 0.001 TYR B1022 PHE 0.019 0.002 PHE A 443 TRP 0.009 0.001 TRP B 311 HIS 0.003 0.001 HIS C1224 Details of bonding type rmsd covalent geometry : bond 0.00517 (24339) covalent geometry : angle 0.75084 (33222) SS BOND : bond 0.04029 ( 42) SS BOND : angle 3.11637 ( 84) hydrogen bonds : bond 0.12221 ( 937) hydrogen bonds : angle 5.59775 ( 2910) link_ALPHA1-3 : bond 0.04440 ( 6) link_ALPHA1-3 : angle 5.37167 ( 18) link_ALPHA1-6 : bond 0.03766 ( 3) link_ALPHA1-6 : angle 4.11908 ( 9) link_BETA1-4 : bond 0.02732 ( 51) link_BETA1-4 : angle 3.39849 ( 153) link_NAG-ASN : bond 0.00268 ( 60) link_NAG-ASN : angle 1.99471 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 257 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 338 LEU cc_start: 0.8037 (mp) cc_final: 0.7704 (mt) REVERT: A 480 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8365 (m-40) REVERT: A 649 ARG cc_start: 0.8678 (ttm170) cc_final: 0.8444 (ttp-170) REVERT: A 909 MET cc_start: 0.8814 (ttt) cc_final: 0.8587 (ttt) REVERT: A 963 ARG cc_start: 0.7400 (mmt90) cc_final: 0.6984 (tpt170) REVERT: A 993 TYR cc_start: 0.7981 (m-80) cc_final: 0.7604 (m-80) REVERT: A 1054 TYR cc_start: 0.8390 (t80) cc_final: 0.7760 (m-80) REVERT: A 1117 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7757 (tm-30) REVERT: A 1304 GLU cc_start: 0.8201 (pt0) cc_final: 0.7949 (pt0) REVERT: B 334 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7755 (p0) REVERT: B 522 LYS cc_start: 0.8671 (mttp) cc_final: 0.8376 (tmtm) REVERT: B 557 LEU cc_start: 0.8465 (mt) cc_final: 0.8253 (mt) REVERT: B 822 PHE cc_start: 0.8294 (t80) cc_final: 0.8081 (t80) REVERT: B 876 ARG cc_start: 0.8193 (mtt180) cc_final: 0.7817 (ttp-170) REVERT: B 963 ARG cc_start: 0.7339 (mmt90) cc_final: 0.6957 (mpt180) REVERT: B 984 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7323 (mt-10) REVERT: B 1054 TYR cc_start: 0.8338 (t80) cc_final: 0.7820 (m-80) REVERT: B 1117 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7720 (tm130) REVERT: C 266 ASN cc_start: 0.7744 (m-40) cc_final: 0.7478 (m110) REVERT: C 323 PHE cc_start: 0.8180 (t80) cc_final: 0.7968 (t80) REVERT: C 480 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8329 (t0) REVERT: C 522 LYS cc_start: 0.8609 (mttp) cc_final: 0.8316 (tmtm) REVERT: C 984 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7369 (mt-10) REVERT: C 1054 TYR cc_start: 0.8371 (t80) cc_final: 0.7802 (m-80) REVERT: C 1117 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7700 (tm130) outliers start: 31 outliers final: 9 residues processed: 282 average time/residue: 0.5552 time to fit residues: 180.8176 Evaluate side-chains 214 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain B residue 972 ASP Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 972 ASP Chi-restraints excluded: chain C residue 1124 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 308 ASN A 584 HIS A1066 GLN B 284 ASN B 308 ASN B 584 HIS B1129 ASN C 284 ASN C 308 ASN C 584 HIS C1015 ASN C1066 GLN C1129 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.144202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118334 restraints weight = 27898.978| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.93 r_work: 0.3287 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24501 Z= 0.137 Angle : 0.561 6.311 33666 Z= 0.279 Chirality : 0.044 0.183 4275 Planarity : 0.004 0.074 4071 Dihedral : 9.577 72.232 5756 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.22 % Allowed : 7.90 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.15), residues: 2952 helix: 2.45 (0.20), residues: 702 sheet: 0.43 (0.18), residues: 753 loop : -0.60 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1174 TYR 0.017 0.002 TYR A1022 PHE 0.013 0.001 PHE B 323 TRP 0.007 0.001 TRP A 432 HIS 0.003 0.001 HIS C1208 Details of bonding type rmsd covalent geometry : bond 0.00308 (24339) covalent geometry : angle 0.52856 (33222) SS BOND : bond 0.00339 ( 42) SS BOND : angle 1.19966 ( 84) hydrogen bonds : bond 0.05326 ( 937) hydrogen bonds : angle 4.61262 ( 2910) link_ALPHA1-3 : bond 0.01193 ( 6) link_ALPHA1-3 : angle 1.23012 ( 18) link_ALPHA1-6 : bond 0.00738 ( 3) link_ALPHA1-6 : angle 1.25114 ( 9) link_BETA1-4 : bond 0.00473 ( 51) link_BETA1-4 : angle 1.98539 ( 153) link_NAG-ASN : bond 0.00292 ( 60) link_NAG-ASN : angle 1.71819 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 213 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 334 ASN cc_start: 0.7741 (OUTLIER) cc_final: 0.7458 (p0) REVERT: A 649 ARG cc_start: 0.8612 (ttm170) cc_final: 0.8193 (ttp-110) REVERT: A 963 ARG cc_start: 0.7569 (mmt90) cc_final: 0.7155 (tpt170) REVERT: A 993 TYR cc_start: 0.8188 (m-80) cc_final: 0.7875 (m-80) REVERT: A 1054 TYR cc_start: 0.8377 (t80) cc_final: 0.7658 (m-80) REVERT: A 1117 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7755 (tm-30) REVERT: A 1143 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8325 (mtp180) REVERT: A 1221 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8714 (pp) REVERT: B 334 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7634 (p0) REVERT: B 477 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8856 (tt0) REVERT: B 522 LYS cc_start: 0.8844 (mttp) cc_final: 0.8355 (tttm) REVERT: B 557 LEU cc_start: 0.8504 (mt) cc_final: 0.8289 (mt) REVERT: B 564 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7775 (tmm) REVERT: B 649 ARG cc_start: 0.8432 (ttp-170) cc_final: 0.7998 (ttm170) REVERT: B 822 PHE cc_start: 0.8317 (t80) cc_final: 0.8115 (t80) REVERT: B 876 ARG cc_start: 0.8337 (mtt180) cc_final: 0.7957 (ttp-170) REVERT: B 902 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8508 (tt0) REVERT: B 963 ARG cc_start: 0.7391 (mmt90) cc_final: 0.7112 (mpt180) REVERT: B 984 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7131 (mt-10) REVERT: B 1054 TYR cc_start: 0.8300 (t80) cc_final: 0.7730 (m-80) REVERT: B 1117 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7713 (tm130) REVERT: B 1143 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8360 (mtt180) REVERT: C 298 ARG cc_start: 0.8874 (mtt90) cc_final: 0.8579 (mtt90) REVERT: C 334 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7401 (p0) REVERT: C 544 MET cc_start: 0.8857 (mmm) cc_final: 0.8505 (mmm) REVERT: C 564 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.8064 (tmm) REVERT: C 893 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8689 (tt0) REVERT: C 984 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7135 (mt-10) REVERT: C 993 TYR cc_start: 0.8033 (m-80) cc_final: 0.7825 (m-80) REVERT: C 1054 TYR cc_start: 0.8350 (t80) cc_final: 0.7743 (m-80) REVERT: C 1117 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7644 (tm130) REVERT: C 1221 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8664 (pp) outliers start: 50 outliers final: 19 residues processed: 249 average time/residue: 0.6104 time to fit residues: 174.3488 Evaluate side-chains 234 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 905 GLU Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain A residue 1221 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 765 GLU Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain B residue 902 GLU Chi-restraints excluded: chain B residue 905 GLU Chi-restraints excluded: chain B residue 972 ASP Chi-restraints excluded: chain B residue 1143 ARG Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 564 MET Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 765 GLU Chi-restraints excluded: chain C residue 862 VAL Chi-restraints excluded: chain C residue 893 GLN Chi-restraints excluded: chain C residue 905 GLU Chi-restraints excluded: chain C residue 972 ASP Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1221 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 80 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 163 optimal weight: 0.2980 chunk 151 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 HIS A1066 GLN B 584 HIS B1129 ASN B1170 GLN C 584 HIS C1015 ASN C1066 GLN C1129 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.137287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109043 restraints weight = 27632.540| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.06 r_work: 0.3188 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 24501 Z= 0.238 Angle : 0.665 7.562 33666 Z= 0.334 Chirality : 0.048 0.194 4275 Planarity : 0.005 0.064 4071 Dihedral : 8.811 68.358 5751 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.09 % Allowed : 8.26 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.15), residues: 2952 helix: 2.03 (0.20), residues: 702 sheet: 0.44 (0.18), residues: 723 loop : -0.81 (0.14), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1199 TYR 0.018 0.002 TYR B 718 PHE 0.014 0.002 PHE B 925 TRP 0.009 0.002 TRP C 945 HIS 0.006 0.001 HIS C1224 Details of bonding type rmsd covalent geometry : bond 0.00559 (24339) covalent geometry : angle 0.63185 (33222) SS BOND : bond 0.00655 ( 42) SS BOND : angle 1.53789 ( 84) hydrogen bonds : bond 0.06956 ( 937) hydrogen bonds : angle 4.91730 ( 2910) link_ALPHA1-3 : bond 0.01039 ( 6) link_ALPHA1-3 : angle 1.15592 ( 18) link_ALPHA1-6 : bond 0.01123 ( 3) link_ALPHA1-6 : angle 1.04436 ( 9) link_BETA1-4 : bond 0.00457 ( 51) link_BETA1-4 : angle 1.98732 ( 153) link_NAG-ASN : bond 0.00428 ( 60) link_NAG-ASN : angle 2.09712 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 213 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 338 LEU cc_start: 0.8196 (mp) cc_final: 0.7820 (mt) REVERT: A 649 ARG cc_start: 0.8639 (ttm170) cc_final: 0.8232 (ttp-110) REVERT: A 963 ARG cc_start: 0.7563 (mmt90) cc_final: 0.7184 (mpt180) REVERT: A 993 TYR cc_start: 0.8179 (m-80) cc_final: 0.7817 (m-80) REVERT: A 1008 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8775 (mtt) REVERT: A 1054 TYR cc_start: 0.8402 (t80) cc_final: 0.7773 (m-80) REVERT: A 1117 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7702 (tm-30) REVERT: A 1143 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8272 (mtp180) REVERT: A 1221 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8783 (pp) REVERT: B 334 ASN cc_start: 0.8008 (OUTLIER) cc_final: 0.7670 (p0) REVERT: B 477 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8788 (tt0) REVERT: B 531 TYR cc_start: 0.8285 (m-10) cc_final: 0.7613 (t80) REVERT: B 557 LEU cc_start: 0.8554 (mt) cc_final: 0.8328 (mt) REVERT: B 564 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7752 (tmm) REVERT: B 649 ARG cc_start: 0.8453 (ttp-170) cc_final: 0.7988 (ttm170) REVERT: B 699 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8358 (mmpt) REVERT: B 876 ARG cc_start: 0.8421 (mtt180) cc_final: 0.8038 (ttp-170) REVERT: B 902 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8603 (tt0) REVERT: B 963 ARG cc_start: 0.7600 (mmt90) cc_final: 0.7187 (mpt180) REVERT: B 984 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7182 (mt-10) REVERT: B 1015 ASN cc_start: 0.8052 (m-40) cc_final: 0.7613 (t0) REVERT: B 1054 TYR cc_start: 0.8426 (t80) cc_final: 0.7844 (m-80) REVERT: B 1117 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7786 (tm130) REVERT: C 334 ASN cc_start: 0.7728 (OUTLIER) cc_final: 0.7320 (p0) REVERT: C 893 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8765 (tt0) REVERT: C 993 TYR cc_start: 0.8153 (m-80) cc_final: 0.7917 (m-80) REVERT: C 1054 TYR cc_start: 0.8410 (t80) cc_final: 0.7850 (m-80) REVERT: C 1117 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7543 (tm-30) REVERT: C 1221 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8743 (pp) outliers start: 47 outliers final: 22 residues processed: 254 average time/residue: 0.5672 time to fit residues: 165.8579 Evaluate side-chains 229 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 905 GLU Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain A residue 1221 ILE Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain B residue 765 GLU Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 902 GLU Chi-restraints excluded: chain B residue 905 GLU Chi-restraints excluded: chain B residue 972 ASP Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 862 VAL Chi-restraints excluded: chain C residue 893 GLN Chi-restraints excluded: chain C residue 905 GLU Chi-restraints excluded: chain C residue 972 ASP Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1221 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 267 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 230 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 293 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 227 optimal weight: 0.0570 chunk 254 optimal weight: 0.6980 chunk 273 optimal weight: 0.2980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 HIS A1066 GLN B 584 HIS B1129 ASN C 284 ASN C 584 HIS C 872 ASN C1015 ASN C1066 GLN C1129 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.141398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113651 restraints weight = 27586.969| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.05 r_work: 0.3253 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 24501 Z= 0.106 Angle : 0.526 12.251 33666 Z= 0.265 Chirality : 0.044 0.240 4275 Planarity : 0.004 0.053 4071 Dihedral : 7.371 61.262 5750 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.86 % Allowed : 9.10 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.15), residues: 2952 helix: 2.43 (0.20), residues: 702 sheet: 0.47 (0.19), residues: 702 loop : -0.74 (0.14), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1182 TYR 0.012 0.001 TYR A1022 PHE 0.010 0.001 PHE A1223 TRP 0.005 0.001 TRP A 432 HIS 0.002 0.000 HIS B1208 Details of bonding type rmsd covalent geometry : bond 0.00223 (24339) covalent geometry : angle 0.49609 (33222) SS BOND : bond 0.00472 ( 42) SS BOND : angle 1.71149 ( 84) hydrogen bonds : bond 0.04808 ( 937) hydrogen bonds : angle 4.45936 ( 2910) link_ALPHA1-3 : bond 0.01202 ( 6) link_ALPHA1-3 : angle 1.17929 ( 18) link_ALPHA1-6 : bond 0.01194 ( 3) link_ALPHA1-6 : angle 1.02314 ( 9) link_BETA1-4 : bond 0.00500 ( 51) link_BETA1-4 : angle 1.59597 ( 153) link_NAG-ASN : bond 0.00278 ( 60) link_NAG-ASN : angle 1.60906 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 338 LEU cc_start: 0.8133 (mp) cc_final: 0.7729 (mt) REVERT: A 649 ARG cc_start: 0.8593 (ttm170) cc_final: 0.8181 (ttp-110) REVERT: A 699 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8519 (mtpt) REVERT: A 963 ARG cc_start: 0.7496 (mmt90) cc_final: 0.7130 (tpt170) REVERT: A 993 TYR cc_start: 0.8165 (m-80) cc_final: 0.7789 (m-80) REVERT: A 1008 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8730 (mtt) REVERT: A 1054 TYR cc_start: 0.8329 (t80) cc_final: 0.7567 (m-80) REVERT: A 1117 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7710 (tm-30) REVERT: A 1143 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8281 (mtp180) REVERT: A 1221 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8626 (pp) REVERT: B 477 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8868 (tt0) REVERT: B 522 LYS cc_start: 0.8787 (mttp) cc_final: 0.8289 (tmtm) REVERT: B 557 LEU cc_start: 0.8461 (mt) cc_final: 0.8259 (mt) REVERT: B 649 ARG cc_start: 0.8399 (ttp-170) cc_final: 0.7962 (ttm170) REVERT: B 876 ARG cc_start: 0.8312 (mtt180) cc_final: 0.7998 (ttp-170) REVERT: B 902 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8477 (tt0) REVERT: B 963 ARG cc_start: 0.7478 (mmt90) cc_final: 0.7163 (mpt180) REVERT: B 984 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7169 (mt-10) REVERT: B 1008 MET cc_start: 0.8811 (mtt) cc_final: 0.8599 (mtt) REVERT: B 1015 ASN cc_start: 0.7956 (m-40) cc_final: 0.7626 (t0) REVERT: B 1054 TYR cc_start: 0.8273 (t80) cc_final: 0.7642 (m-80) REVERT: B 1117 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7681 (tm130) REVERT: C 334 ASN cc_start: 0.7573 (OUTLIER) cc_final: 0.7260 (p0) REVERT: C 993 TYR cc_start: 0.8077 (m-80) cc_final: 0.7863 (m-80) REVERT: C 1054 TYR cc_start: 0.8323 (t80) cc_final: 0.7658 (m-80) REVERT: C 1117 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7548 (tm130) REVERT: C 1174 ARG cc_start: 0.8727 (tpp-160) cc_final: 0.8411 (tpp80) REVERT: C 1221 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8632 (pp) outliers start: 42 outliers final: 14 residues processed: 250 average time/residue: 0.5536 time to fit residues: 159.8229 Evaluate side-chains 230 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain A residue 905 GLU Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1019 MET Chi-restraints excluded: chain A residue 1066 GLN Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain A residue 1221 ILE Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain B residue 765 GLU Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 902 GLU Chi-restraints excluded: chain B residue 905 GLU Chi-restraints excluded: chain B residue 972 ASP Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 905 GLU Chi-restraints excluded: chain C residue 972 ASP Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1221 ILE Chi-restraints excluded: chain C residue 1260 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 289 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 175 optimal weight: 4.9990 chunk 226 optimal weight: 4.9990 chunk 249 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 286 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 584 HIS A1066 GLN B 308 ASN B 584 HIS B1129 ASN C 584 HIS C1066 GLN C1129 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.139581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.111574 restraints weight = 27683.349| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.06 r_work: 0.3217 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24501 Z= 0.146 Angle : 0.564 10.668 33666 Z= 0.284 Chirality : 0.044 0.212 4275 Planarity : 0.004 0.053 4071 Dihedral : 7.155 59.455 5746 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.91 % Allowed : 9.05 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.15), residues: 2952 helix: 2.37 (0.20), residues: 702 sheet: 0.39 (0.19), residues: 696 loop : -0.73 (0.14), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 298 TYR 0.015 0.002 TYR B1022 PHE 0.008 0.001 PHE C 644 TRP 0.006 0.001 TRP A 432 HIS 0.004 0.001 HIS B1224 Details of bonding type rmsd covalent geometry : bond 0.00331 (24339) covalent geometry : angle 0.53411 (33222) SS BOND : bond 0.00559 ( 42) SS BOND : angle 1.63363 ( 84) hydrogen bonds : bond 0.05483 ( 937) hydrogen bonds : angle 4.58121 ( 2910) link_ALPHA1-3 : bond 0.01194 ( 6) link_ALPHA1-3 : angle 1.17677 ( 18) link_ALPHA1-6 : bond 0.01336 ( 3) link_ALPHA1-6 : angle 0.87857 ( 9) link_BETA1-4 : bond 0.00443 ( 51) link_BETA1-4 : angle 1.67399 ( 153) link_NAG-ASN : bond 0.00297 ( 60) link_NAG-ASN : angle 1.75435 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 212 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 332 GLN cc_start: 0.5777 (OUTLIER) cc_final: 0.4794 (tm-30) REVERT: A 338 LEU cc_start: 0.8126 (mp) cc_final: 0.7699 (mt) REVERT: A 649 ARG cc_start: 0.8608 (ttm170) cc_final: 0.8191 (ttp-110) REVERT: A 699 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8458 (mtpt) REVERT: A 963 ARG cc_start: 0.7527 (mmt90) cc_final: 0.7165 (tpt170) REVERT: A 993 TYR cc_start: 0.8194 (m-80) cc_final: 0.7852 (m-80) REVERT: A 1008 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8733 (mtt) REVERT: A 1054 TYR cc_start: 0.8365 (t80) cc_final: 0.7663 (m-80) REVERT: A 1117 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7692 (tm-30) REVERT: A 1143 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8292 (mtp180) REVERT: A 1221 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8747 (pp) REVERT: B 477 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8862 (tt0) REVERT: B 557 LEU cc_start: 0.8486 (mt) cc_final: 0.8283 (mt) REVERT: B 564 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7801 (tmm) REVERT: B 649 ARG cc_start: 0.8398 (ttp-170) cc_final: 0.7950 (ttm170) REVERT: B 699 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8298 (mmpt) REVERT: B 876 ARG cc_start: 0.8387 (mtt180) cc_final: 0.8062 (ttp-170) REVERT: B 902 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8491 (tt0) REVERT: B 963 ARG cc_start: 0.7526 (mmt90) cc_final: 0.7172 (mpt180) REVERT: B 984 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7191 (mt-10) REVERT: B 1015 ASN cc_start: 0.7965 (m-40) cc_final: 0.7648 (t0) REVERT: B 1054 TYR cc_start: 0.8263 (t80) cc_final: 0.7700 (m-80) REVERT: B 1117 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7733 (tm130) REVERT: C 316 PHE cc_start: 0.8671 (m-80) cc_final: 0.8427 (m-80) REVERT: C 334 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.7230 (p0) REVERT: C 993 TYR cc_start: 0.8120 (m-80) cc_final: 0.7902 (m-80) REVERT: C 1054 TYR cc_start: 0.8372 (t80) cc_final: 0.7699 (m-80) REVERT: C 1117 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7541 (tm130) REVERT: C 1174 ARG cc_start: 0.8697 (tpp-160) cc_final: 0.8389 (tpp80) REVERT: C 1221 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8697 (pp) outliers start: 43 outliers final: 19 residues processed: 247 average time/residue: 0.5661 time to fit residues: 161.4182 Evaluate side-chains 229 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 905 GLU Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1019 MET Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain A residue 1221 ILE Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain B residue 765 GLU Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 902 GLU Chi-restraints excluded: chain B residue 905 GLU Chi-restraints excluded: chain B residue 972 ASP Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 905 GLU Chi-restraints excluded: chain C residue 972 ASP Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1221 ILE Chi-restraints excluded: chain C residue 1260 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 HIS A1066 GLN B 584 HIS B1129 ASN C 266 ASN C 284 ASN C 584 HIS C1015 ASN C1066 GLN C1129 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.140554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112576 restraints weight = 27784.926| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.07 r_work: 0.3231 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24501 Z= 0.124 Angle : 0.540 14.892 33666 Z= 0.272 Chirality : 0.044 0.224 4275 Planarity : 0.004 0.052 4071 Dihedral : 6.765 59.685 5746 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.86 % Allowed : 9.45 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.15), residues: 2952 helix: 2.45 (0.20), residues: 702 sheet: 0.35 (0.19), residues: 696 loop : -0.71 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 298 TYR 0.014 0.001 TYR A1022 PHE 0.008 0.001 PHE B 442 TRP 0.006 0.001 TRP A 432 HIS 0.003 0.001 HIS B1224 Details of bonding type rmsd covalent geometry : bond 0.00269 (24339) covalent geometry : angle 0.51293 (33222) SS BOND : bond 0.00532 ( 42) SS BOND : angle 1.40705 ( 84) hydrogen bonds : bond 0.05104 ( 937) hydrogen bonds : angle 4.50673 ( 2910) link_ALPHA1-3 : bond 0.01229 ( 6) link_ALPHA1-3 : angle 1.25029 ( 18) link_ALPHA1-6 : bond 0.01384 ( 3) link_ALPHA1-6 : angle 0.85026 ( 9) link_BETA1-4 : bond 0.00460 ( 51) link_BETA1-4 : angle 1.56366 ( 153) link_NAG-ASN : bond 0.00278 ( 60) link_NAG-ASN : angle 1.68030 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 0.903 Fit side-chains REVERT: A 266 ASN cc_start: 0.7678 (m110) cc_final: 0.7434 (m-40) REVERT: A 332 GLN cc_start: 0.5787 (OUTLIER) cc_final: 0.4719 (tm-30) REVERT: A 649 ARG cc_start: 0.8611 (ttm170) cc_final: 0.8308 (ttp-110) REVERT: A 699 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8453 (mtpt) REVERT: A 963 ARG cc_start: 0.7513 (mmt90) cc_final: 0.7151 (tpt170) REVERT: A 993 TYR cc_start: 0.8191 (m-80) cc_final: 0.7849 (m-80) REVERT: A 1054 TYR cc_start: 0.8363 (t80) cc_final: 0.7617 (m-80) REVERT: A 1117 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7700 (tm-30) REVERT: A 1143 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8300 (mtp180) REVERT: A 1221 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8708 (pp) REVERT: B 477 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8867 (tt0) REVERT: B 557 LEU cc_start: 0.8472 (mt) cc_final: 0.8268 (mt) REVERT: B 564 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7760 (tmm) REVERT: B 649 ARG cc_start: 0.8386 (ttp-170) cc_final: 0.7963 (ttm170) REVERT: B 699 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8290 (mmpt) REVERT: B 876 ARG cc_start: 0.8371 (mtt180) cc_final: 0.8078 (ttp-170) REVERT: B 902 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8480 (tt0) REVERT: B 963 ARG cc_start: 0.7539 (mmt90) cc_final: 0.7200 (mpt180) REVERT: B 984 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7194 (mt-10) REVERT: B 1015 ASN cc_start: 0.7901 (m-40) cc_final: 0.7623 (t0) REVERT: B 1054 TYR cc_start: 0.8273 (t80) cc_final: 0.7645 (m-80) REVERT: B 1117 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7688 (tm130) REVERT: C 316 PHE cc_start: 0.8656 (m-80) cc_final: 0.8387 (m-80) REVERT: C 334 ASN cc_start: 0.7560 (OUTLIER) cc_final: 0.7154 (p0) REVERT: C 1054 TYR cc_start: 0.8323 (t80) cc_final: 0.7689 (m-80) REVERT: C 1117 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7540 (tm130) REVERT: C 1174 ARG cc_start: 0.8711 (tpp-160) cc_final: 0.8411 (tpp80) REVERT: C 1221 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8696 (pp) outliers start: 42 outliers final: 20 residues processed: 242 average time/residue: 0.5735 time to fit residues: 160.3311 Evaluate side-chains 234 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 905 GLU Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1019 MET Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain A residue 1221 ILE Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 902 GLU Chi-restraints excluded: chain B residue 905 GLU Chi-restraints excluded: chain B residue 972 ASP Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 905 GLU Chi-restraints excluded: chain C residue 972 ASP Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1221 ILE Chi-restraints excluded: chain C residue 1260 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 22 optimal weight: 0.9990 chunk 258 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 272 optimal weight: 0.8980 chunk 266 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 294 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 584 HIS A1066 GLN B 584 HIS B1129 ASN C 584 HIS C1066 GLN C1129 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110667 restraints weight = 27554.694| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.06 r_work: 0.3200 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24501 Z= 0.167 Angle : 0.586 15.164 33666 Z= 0.295 Chirality : 0.045 0.219 4275 Planarity : 0.004 0.053 4071 Dihedral : 6.850 59.414 5746 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.95 % Allowed : 9.50 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.15), residues: 2952 helix: 2.30 (0.20), residues: 702 sheet: 0.34 (0.19), residues: 693 loop : -0.78 (0.14), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 298 TYR 0.015 0.002 TYR A 809 PHE 0.010 0.002 PHE A 644 TRP 0.006 0.001 TRP A 432 HIS 0.004 0.001 HIS B1224 Details of bonding type rmsd covalent geometry : bond 0.00382 (24339) covalent geometry : angle 0.55868 (33222) SS BOND : bond 0.00653 ( 42) SS BOND : angle 1.47864 ( 84) hydrogen bonds : bond 0.05833 ( 937) hydrogen bonds : angle 4.66317 ( 2910) link_ALPHA1-3 : bond 0.01103 ( 6) link_ALPHA1-3 : angle 1.20685 ( 18) link_ALPHA1-6 : bond 0.01472 ( 3) link_ALPHA1-6 : angle 0.77318 ( 9) link_BETA1-4 : bond 0.00441 ( 51) link_BETA1-4 : angle 1.65606 ( 153) link_NAG-ASN : bond 0.00330 ( 60) link_NAG-ASN : angle 1.77642 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 0.752 Fit side-chains REVERT: A 332 GLN cc_start: 0.5762 (OUTLIER) cc_final: 0.4753 (tm-30) REVERT: A 338 LEU cc_start: 0.8074 (mp) cc_final: 0.7730 (mt) REVERT: A 649 ARG cc_start: 0.8593 (ttm170) cc_final: 0.8274 (ttp-110) REVERT: A 699 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8468 (mtpt) REVERT: A 963 ARG cc_start: 0.7528 (mmt90) cc_final: 0.7151 (mpt180) REVERT: A 993 TYR cc_start: 0.8221 (m-80) cc_final: 0.7847 (m-80) REVERT: A 1054 TYR cc_start: 0.8368 (t80) cc_final: 0.7667 (m-80) REVERT: A 1117 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7669 (tm-30) REVERT: A 1143 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8309 (mtp180) REVERT: A 1221 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8709 (pp) REVERT: B 477 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8876 (tt0) REVERT: B 564 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7754 (tmm) REVERT: B 649 ARG cc_start: 0.8409 (ttp-170) cc_final: 0.7975 (ttm170) REVERT: B 699 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8268 (mmpt) REVERT: B 876 ARG cc_start: 0.8377 (mtt180) cc_final: 0.8074 (ttp-170) REVERT: B 902 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8505 (tt0) REVERT: B 963 ARG cc_start: 0.7572 (mmt90) cc_final: 0.7220 (mpt180) REVERT: B 984 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7172 (mt-10) REVERT: B 1015 ASN cc_start: 0.7975 (m-40) cc_final: 0.7653 (t0) REVERT: B 1054 TYR cc_start: 0.8267 (t80) cc_final: 0.7679 (m-80) REVERT: B 1117 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7785 (tm130) REVERT: C 316 PHE cc_start: 0.8673 (m-80) cc_final: 0.8434 (m-80) REVERT: C 334 ASN cc_start: 0.7640 (OUTLIER) cc_final: 0.7159 (p0) REVERT: C 1054 TYR cc_start: 0.8351 (t80) cc_final: 0.7728 (m-80) REVERT: C 1117 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7558 (tm130) REVERT: C 1174 ARG cc_start: 0.8731 (tpp-160) cc_final: 0.8423 (tpp80) REVERT: C 1221 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8710 (pp) outliers start: 44 outliers final: 24 residues processed: 242 average time/residue: 0.5654 time to fit residues: 157.8710 Evaluate side-chains 235 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain A residue 893 GLN Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 905 GLU Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1019 MET Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain A residue 1221 ILE Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain B residue 902 GLU Chi-restraints excluded: chain B residue 905 GLU Chi-restraints excluded: chain B residue 972 ASP Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 905 GLU Chi-restraints excluded: chain C residue 972 ASP Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1221 ILE Chi-restraints excluded: chain C residue 1260 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 183 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 222 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 139 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 270 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 159 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 HIS A1066 GLN B 584 HIS B1129 ASN C 266 ASN C 284 ASN C 584 HIS C1015 ASN C1066 GLN C1129 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.140821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112922 restraints weight = 27535.420| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.06 r_work: 0.3238 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24501 Z= 0.114 Angle : 0.524 12.995 33666 Z= 0.265 Chirality : 0.043 0.232 4275 Planarity : 0.004 0.053 4071 Dihedral : 6.428 57.417 5746 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.86 % Allowed : 9.76 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.15), residues: 2952 helix: 2.48 (0.20), residues: 702 sheet: 0.35 (0.19), residues: 696 loop : -0.70 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 298 TYR 0.014 0.001 TYR A1022 PHE 0.008 0.001 PHE B 442 TRP 0.006 0.001 TRP A 432 HIS 0.002 0.001 HIS B1224 Details of bonding type rmsd covalent geometry : bond 0.00243 (24339) covalent geometry : angle 0.49777 (33222) SS BOND : bond 0.00528 ( 42) SS BOND : angle 1.15460 ( 84) hydrogen bonds : bond 0.04955 ( 937) hydrogen bonds : angle 4.49296 ( 2910) link_ALPHA1-3 : bond 0.01159 ( 6) link_ALPHA1-3 : angle 1.31831 ( 18) link_ALPHA1-6 : bond 0.01433 ( 3) link_ALPHA1-6 : angle 0.84366 ( 9) link_BETA1-4 : bond 0.00469 ( 51) link_BETA1-4 : angle 1.49560 ( 153) link_NAG-ASN : bond 0.00267 ( 60) link_NAG-ASN : angle 1.68736 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 0.750 Fit side-chains REVERT: A 332 GLN cc_start: 0.5717 (OUTLIER) cc_final: 0.4822 (tm-30) REVERT: A 338 LEU cc_start: 0.8097 (mp) cc_final: 0.7754 (mt) REVERT: A 649 ARG cc_start: 0.8579 (ttm170) cc_final: 0.8268 (ttp-110) REVERT: A 699 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8493 (mtpt) REVERT: A 963 ARG cc_start: 0.7508 (mmt90) cc_final: 0.7135 (tpt170) REVERT: A 993 TYR cc_start: 0.8189 (m-80) cc_final: 0.7847 (m-80) REVERT: A 1054 TYR cc_start: 0.8341 (t80) cc_final: 0.7602 (m-80) REVERT: A 1117 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7719 (tm-30) REVERT: A 1143 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8302 (mtp180) REVERT: A 1221 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8697 (pp) REVERT: B 477 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8872 (tt0) REVERT: B 564 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7715 (tmm) REVERT: B 649 ARG cc_start: 0.8368 (ttp-170) cc_final: 0.7951 (ttm170) REVERT: B 699 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8254 (mmpt) REVERT: B 876 ARG cc_start: 0.8368 (mtt180) cc_final: 0.8090 (ttp-170) REVERT: B 902 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8472 (tt0) REVERT: B 963 ARG cc_start: 0.7617 (mmt90) cc_final: 0.7186 (mpt180) REVERT: B 984 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7181 (mt-10) REVERT: B 1015 ASN cc_start: 0.7901 (m-40) cc_final: 0.7648 (t0) REVERT: B 1054 TYR cc_start: 0.8252 (t80) cc_final: 0.7683 (m-80) REVERT: B 1117 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7698 (tm130) REVERT: C 334 ASN cc_start: 0.7536 (OUTLIER) cc_final: 0.7032 (p0) REVERT: C 356 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8012 (mm-40) REVERT: C 1054 TYR cc_start: 0.8303 (t80) cc_final: 0.7669 (m-80) REVERT: C 1109 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: C 1117 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7556 (tm130) REVERT: C 1174 ARG cc_start: 0.8709 (tpp-160) cc_final: 0.8420 (tpp80) REVERT: C 1221 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8686 (pp) outliers start: 42 outliers final: 20 residues processed: 242 average time/residue: 0.5717 time to fit residues: 159.3750 Evaluate side-chains 238 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 905 GLU Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1019 MET Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain A residue 1221 ILE Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 902 GLU Chi-restraints excluded: chain B residue 905 GLU Chi-restraints excluded: chain B residue 972 ASP Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 905 GLU Chi-restraints excluded: chain C residue 972 ASP Chi-restraints excluded: chain C residue 1109 GLN Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1221 ILE Chi-restraints excluded: chain C residue 1260 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 258 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 270 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 293 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 HIS A1066 GLN B 584 HIS B1129 ASN C 584 HIS C1066 GLN C1129 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.139044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110851 restraints weight = 27596.253| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.06 r_work: 0.3201 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24501 Z= 0.161 Angle : 0.575 14.016 33666 Z= 0.290 Chirality : 0.045 0.223 4275 Planarity : 0.004 0.053 4071 Dihedral : 6.534 54.706 5746 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.78 % Allowed : 10.08 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.15), residues: 2952 helix: 2.31 (0.20), residues: 702 sheet: 0.33 (0.19), residues: 693 loop : -0.77 (0.14), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 298 TYR 0.015 0.002 TYR A 809 PHE 0.010 0.001 PHE A 644 TRP 0.006 0.001 TRP A 432 HIS 0.003 0.001 HIS B1224 Details of bonding type rmsd covalent geometry : bond 0.00366 (24339) covalent geometry : angle 0.54811 (33222) SS BOND : bond 0.00614 ( 42) SS BOND : angle 1.31422 ( 84) hydrogen bonds : bond 0.05744 ( 937) hydrogen bonds : angle 4.66733 ( 2910) link_ALPHA1-3 : bond 0.01035 ( 6) link_ALPHA1-3 : angle 1.24508 ( 18) link_ALPHA1-6 : bond 0.01513 ( 3) link_ALPHA1-6 : angle 0.75083 ( 9) link_BETA1-4 : bond 0.00441 ( 51) link_BETA1-4 : angle 1.61623 ( 153) link_NAG-ASN : bond 0.00326 ( 60) link_NAG-ASN : angle 1.76878 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 0.858 Fit side-chains REVERT: A 332 GLN cc_start: 0.5754 (OUTLIER) cc_final: 0.4827 (tm-30) REVERT: A 338 LEU cc_start: 0.8130 (mp) cc_final: 0.7754 (mt) REVERT: A 649 ARG cc_start: 0.8603 (ttm170) cc_final: 0.8284 (ttp-110) REVERT: A 699 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8460 (mtpt) REVERT: A 963 ARG cc_start: 0.7534 (mmt90) cc_final: 0.7158 (tpt170) REVERT: A 993 TYR cc_start: 0.8218 (m-80) cc_final: 0.7861 (m-80) REVERT: A 1054 TYR cc_start: 0.8363 (t80) cc_final: 0.7659 (m-80) REVERT: A 1117 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7674 (tm-30) REVERT: A 1143 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8306 (mtp180) REVERT: A 1221 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8753 (pp) REVERT: B 477 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8868 (tt0) REVERT: B 564 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7745 (tmm) REVERT: B 649 ARG cc_start: 0.8400 (ttp-170) cc_final: 0.7968 (ttm170) REVERT: B 699 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8262 (mmpt) REVERT: B 876 ARG cc_start: 0.8380 (mtt180) cc_final: 0.8090 (ttp-170) REVERT: B 902 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8503 (tt0) REVERT: B 963 ARG cc_start: 0.7661 (mmt90) cc_final: 0.7232 (mpt180) REVERT: B 984 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7190 (mt-10) REVERT: B 1015 ASN cc_start: 0.7965 (m-40) cc_final: 0.7673 (t0) REVERT: B 1054 TYR cc_start: 0.8266 (t80) cc_final: 0.7711 (m-80) REVERT: B 1117 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7785 (tm130) REVERT: C 334 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.7067 (p0) REVERT: C 1054 TYR cc_start: 0.8352 (t80) cc_final: 0.7730 (m-80) REVERT: C 1109 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7646 (mp10) REVERT: C 1117 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7550 (tm130) REVERT: C 1221 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8699 (pp) outliers start: 40 outliers final: 24 residues processed: 238 average time/residue: 0.6119 time to fit residues: 166.9860 Evaluate side-chains 236 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain A residue 893 GLN Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 905 GLU Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1019 MET Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain A residue 1221 ILE Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 902 GLU Chi-restraints excluded: chain B residue 905 GLU Chi-restraints excluded: chain B residue 972 ASP Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 905 GLU Chi-restraints excluded: chain C residue 972 ASP Chi-restraints excluded: chain C residue 1109 GLN Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1221 ILE Chi-restraints excluded: chain C residue 1260 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 136 optimal weight: 0.0050 chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 245 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 HIS A1066 GLN B 584 HIS B1129 ASN C 584 HIS C1066 GLN C1129 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.138365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.110115 restraints weight = 27637.831| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.07 r_work: 0.3194 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24501 Z= 0.182 Angle : 0.598 13.848 33666 Z= 0.302 Chirality : 0.045 0.222 4275 Planarity : 0.004 0.054 4071 Dihedral : 6.599 57.436 5746 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.78 % Allowed : 10.39 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.15), residues: 2952 helix: 2.24 (0.20), residues: 699 sheet: 0.32 (0.18), residues: 714 loop : -0.79 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 298 TYR 0.016 0.002 TYR A 809 PHE 0.011 0.002 PHE A 644 TRP 0.006 0.001 TRP C 945 HIS 0.004 0.001 HIS B1224 Details of bonding type rmsd covalent geometry : bond 0.00418 (24339) covalent geometry : angle 0.57108 (33222) SS BOND : bond 0.00644 ( 42) SS BOND : angle 1.35175 ( 84) hydrogen bonds : bond 0.06079 ( 937) hydrogen bonds : angle 4.74261 ( 2910) link_ALPHA1-3 : bond 0.00998 ( 6) link_ALPHA1-3 : angle 1.24479 ( 18) link_ALPHA1-6 : bond 0.01548 ( 3) link_ALPHA1-6 : angle 0.74397 ( 9) link_BETA1-4 : bond 0.00447 ( 51) link_BETA1-4 : angle 1.65632 ( 153) link_NAG-ASN : bond 0.00356 ( 60) link_NAG-ASN : angle 1.84576 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 0.886 Fit side-chains REVERT: A 332 GLN cc_start: 0.5715 (OUTLIER) cc_final: 0.4812 (tm-30) REVERT: A 338 LEU cc_start: 0.8154 (mp) cc_final: 0.7769 (mt) REVERT: A 649 ARG cc_start: 0.8589 (ttm170) cc_final: 0.8272 (ttp-110) REVERT: A 699 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8474 (mtpt) REVERT: A 963 ARG cc_start: 0.7531 (mmt90) cc_final: 0.7166 (tpt170) REVERT: A 993 TYR cc_start: 0.8221 (m-80) cc_final: 0.7882 (m-80) REVERT: A 1054 TYR cc_start: 0.8373 (t80) cc_final: 0.7689 (m-80) REVERT: A 1117 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7629 (tm-30) REVERT: A 1143 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8309 (mtp180) REVERT: A 1221 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8730 (pp) REVERT: B 477 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8876 (tt0) REVERT: B 564 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7760 (tmm) REVERT: B 649 ARG cc_start: 0.8387 (ttp-170) cc_final: 0.7963 (ttm170) REVERT: B 699 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8243 (mmpt) REVERT: B 876 ARG cc_start: 0.8383 (mtt180) cc_final: 0.8089 (ttp-170) REVERT: B 902 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: B 963 ARG cc_start: 0.7688 (mmt90) cc_final: 0.7266 (mpt180) REVERT: B 984 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7188 (mt-10) REVERT: B 1015 ASN cc_start: 0.7983 (m-40) cc_final: 0.7657 (t0) REVERT: B 1054 TYR cc_start: 0.8259 (t80) cc_final: 0.7688 (m-80) REVERT: B 1117 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7828 (tm130) REVERT: C 334 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7116 (p0) REVERT: C 1054 TYR cc_start: 0.8351 (t80) cc_final: 0.7790 (m-80) REVERT: C 1109 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7651 (mp10) REVERT: C 1117 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7509 (tm130) REVERT: C 1221 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8705 (pp) outliers start: 40 outliers final: 25 residues processed: 241 average time/residue: 0.6251 time to fit residues: 173.1185 Evaluate side-chains 242 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain A residue 893 GLN Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 905 GLU Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1019 MET Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain A residue 1221 ILE Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain B residue 902 GLU Chi-restraints excluded: chain B residue 905 GLU Chi-restraints excluded: chain B residue 972 ASP Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 905 GLU Chi-restraints excluded: chain C residue 972 ASP Chi-restraints excluded: chain C residue 1109 GLN Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1221 ILE Chi-restraints excluded: chain C residue 1260 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 130 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 192 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 50 optimal weight: 0.0970 chunk 9 optimal weight: 0.0570 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 HIS A1066 GLN B 584 HIS B1129 ASN C 266 ASN C 308 ASN C 584 HIS C1066 GLN C1129 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.141412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113644 restraints weight = 27431.454| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.05 r_work: 0.3255 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24501 Z= 0.104 Angle : 0.508 11.698 33666 Z= 0.258 Chirality : 0.043 0.235 4275 Planarity : 0.004 0.054 4071 Dihedral : 5.936 50.422 5746 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.55 % Allowed : 10.56 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.15), residues: 2952 helix: 2.51 (0.20), residues: 702 sheet: 0.35 (0.19), residues: 696 loop : -0.69 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 298 TYR 0.014 0.001 TYR A1022 PHE 0.008 0.001 PHE C 579 TRP 0.006 0.001 TRP C 464 HIS 0.005 0.001 HIS B 584 Details of bonding type rmsd covalent geometry : bond 0.00214 (24339) covalent geometry : angle 0.48520 (33222) SS BOND : bond 0.00561 ( 42) SS BOND : angle 0.99710 ( 84) hydrogen bonds : bond 0.04704 ( 937) hydrogen bonds : angle 4.47457 ( 2910) link_ALPHA1-3 : bond 0.01077 ( 6) link_ALPHA1-3 : angle 1.36582 ( 18) link_ALPHA1-6 : bond 0.01467 ( 3) link_ALPHA1-6 : angle 0.85628 ( 9) link_BETA1-4 : bond 0.00485 ( 51) link_BETA1-4 : angle 1.42231 ( 153) link_NAG-ASN : bond 0.00271 ( 60) link_NAG-ASN : angle 1.56840 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7955.94 seconds wall clock time: 136 minutes 8.89 seconds (8168.89 seconds total)