Starting phenix.real_space_refine on Mon Sep 14 17:23:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6n1w_9320/09_2026/6n1w_9320.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n1w_9320/09_2026/6n1w_9320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n1w_9320/09_2026/6n1w_9320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n1w_9320/09_2026/6n1w_9320.map" model { file = "/net/cci-nas-00/data/ceres_data/6n1w_9320/09_2026/6n1w_9320.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n1w_9320/09_2026/6n1w_9320.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6n1w_9320/09_2026/6n1w_9320.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6n1w_9320/09_2026/6n1w_9320.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 20007 2.51 5 N 5295 2.21 5 O 6435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31905 Number of models: 1 Model: "" Number of chains: 66 Chain: "2" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "3" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 980 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "4" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 787 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "5" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "6" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "7" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "8" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "C" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 980 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "L" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 787 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "Q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "R" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "c" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "d" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "h" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 980 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "l" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 787 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "m" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "n" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "r" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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 chiralities: 2 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "j" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "0" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "1" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "2" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.72, per 1000 atoms: 0.21 Number of scatterers: 31905 At special positions: 0 Unit cell: (159.43, 155.15, 166.92, 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 168 16.00 O 6435 8.00 N 5295 7.00 C 20007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS 2 119 " - pdb=" SG CYS 2 205 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 131 " - pdb=" SG CYS 2 157 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 201 " - pdb=" SG CYS 2 433 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 218 " - pdb=" SG CYS 2 247 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 228 " - pdb=" SG CYS 2 239 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 296 " - pdb=" SG CYS 2 331 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 378 " - pdb=" SG CYS 2 445 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 385 " - pdb=" SG CYS 2 418 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 23 " - pdb=" SG CYS 4 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 22 " - pdb=" SG CYS 5 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 23 " - pdb=" SG CYS 6 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 22 " - pdb=" SG CYS 8 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 98 " - pdb=" SG CYS 8 100A" distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 98 " - pdb=" SG CYS Q 100A" distance=2.03 Simple disulfide: pdb=" SG CYS c 119 " - pdb=" SG CYS c 205 " distance=2.03 Simple disulfide: pdb=" SG CYS c 131 " - pdb=" SG CYS c 157 " distance=2.03 Simple disulfide: pdb=" SG CYS c 201 " - pdb=" SG CYS c 433 " distance=2.03 Simple disulfide: pdb=" SG CYS c 218 " - pdb=" SG CYS c 247 " distance=2.03 Simple disulfide: pdb=" SG CYS c 228 " - pdb=" SG CYS c 239 " distance=2.03 Simple disulfide: pdb=" SG CYS c 296 " - pdb=" SG CYS c 331 " distance=2.03 Simple disulfide: pdb=" SG CYS c 378 " - pdb=" SG CYS c 445 " distance=2.03 Simple disulfide: pdb=" SG CYS c 385 " - pdb=" SG CYS c 418 " distance=2.03 Simple disulfide: pdb=" SG CYS d 598 " - pdb=" SG CYS d 604 " distance=2.02 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.03 Simple disulfide: pdb=" SG CYS m 22 " - pdb=" SG CYS m 92 " distance=2.03 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 88 " distance=2.03 Simple disulfide: pdb=" SG CYS q 22 " - pdb=" SG CYS q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS q 98 " - pdb=" SG CYS q 100A" distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 1 4 " - " MAN 1 5 " " MAN 1 5 " - " MAN 1 6 " " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN j 4 " - " MAN j 5 " " MAN j 5 " - " MAN j 6 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA 1 3 " - " MAN 1 4 " " MAN 1 7 " - " MAN 1 8 " " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 8 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA b 3 " - " MAN b 4 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " " MAN j 7 " - " MAN j 8 " " BMA o 3 " - " MAN o 4 " " BMA s 3 " - " MAN s 4 " " BMA w 3 " - " MAN w 4 " " BMAAA 3 " - " MANAA 4 " ALPHA1-6 " BMA 1 3 " - " MAN 1 7 " " MAN 1 7 " - " MAN 1 9 " " BMA J 3 " - " MAN J 5 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 9 " " BMA b 3 " - " MAN b 5 " " BMA j 3 " - " MAN j 7 " " MAN j 7 " - " MAN j 9 " " BMA w 3 " - " MAN w 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 9 1 " - " NAG 9 2 " " NAG B 1 " - " NAG B 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG 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 Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " NAG-ASN " NAG 0 1 " - " ASN c 386 " " NAG 1 1 " - " ASN c 332 " " NAG 2 611 " - " ASN 2 197 " " NAG 2 623 " - " ASN 2 355 " " NAG 2 631 " - " ASN 2 392 " " NAG B 1 " - " ASN 2 133 " " NAG C 611 " - " ASN C 197 " " NAG C 623 " - " ASN C 355 " " NAG C 631 " - " ASN C 392 " " NAG E 1 " - " ASN 2 137 " " NAG F 1 " - " ASN 2 156 " " NAG G 1 " - " ASN 2 160 " " NAG I 1 " - " ASN 2 234 " " NAG J 1 " - " ASN 2 262 " " NAG K 1 " - " ASN 2 295 " " NAG O 1 " - " ASN 2 301 " " NAG P 1 " - " ASN 2 363 " " NAG S 1 " - " ASN 2 386 " " NAG T 1 " - " ASN 2 332 " " NAG V 1 " - " ASN 2 276 " " NAG W 1 " - " ASN C 133 " " NAG X 1 " - " ASN C 137 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN C 262 " " NAG c 611 " - " ASN c 197 " " NAG c 623 " - " ASN c 355 " " NAG c 631 " - " ASN c 392 " " NAG e 1 " - " ASN C 295 " " NAG f 1 " - " ASN C 301 " " NAG g 1 " - " ASN C 363 " " NAG i 1 " - " ASN C 386 " " NAG j 1 " - " ASN C 332 " " NAG o 1 " - " ASN C 276 " " NAG p 1 " - " ASN c 133 " " NAG s 1 " - " ASN c 137 " " NAG t 1 " - " ASN c 156 " " NAG u 1 " - " ASN c 160 " " NAG v 1 " - " ASN c 234 " " NAG w 1 " - " ASN c 262 " " NAG x 1 " - " ASN c 295 " " NAG y 1 " - " ASN c 301 " " NAG z 1 " - " ASN c 363 " " NAGAA 1 " - " ASN c 276 " Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.4 seconds 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7068 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 79 sheets defined 14.0% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain '2' and resid 58 through 63 removed outlier: 3.779A pdb=" N THR 2 63 " --> pdb=" O LYS 2 59 " (cutoff:3.500A) Processing helix chain '2' and resid 100 through 115 Processing helix chain '2' and resid 122 through 126 removed outlier: 3.992A pdb=" N CYS 2 126 " --> pdb=" O THR 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 195 through 198 removed outlier: 3.719A pdb=" N THR 2 198 " --> pdb=" O ASN 2 195 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 195 through 198' Processing helix chain '2' and resid 335 through 350 Processing helix chain '2' and resid 368 through 373 removed outlier: 3.974A pdb=" N THR 2 372 " --> pdb=" O ASP 2 368 " (cutoff:3.500A) Processing helix chain '2' and resid 425 through 429 removed outlier: 4.121A pdb=" N ARG 2 429 " --> pdb=" O MET 2 426 " (cutoff:3.500A) Processing helix chain '2' and resid 475 through 480 removed outlier: 3.617A pdb=" N TRP 2 479 " --> pdb=" O MET 2 475 " (cutoff:3.500A) Processing helix chain '3' and resid 61 through 64 Processing helix chain '3' and resid 83 through 87 Processing helix chain '4' and resid 79 through 83 removed outlier: 3.709A pdb=" N VAL 4 83 " --> pdb=" O PRO 4 80 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 87 removed outlier: 3.708A pdb=" N SER 5 87 " --> pdb=" O ALA 5 84 " (cutoff:3.500A) Processing helix chain '7' and resid 78 through 82 Processing helix chain '8' and resid 61 through 64 removed outlier: 3.578A pdb=" N GLN 8 64 " --> pdb=" O ARG 8 61 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 61 through 64' Processing helix chain '8' and resid 83 through 87 removed outlier: 3.748A pdb=" N THR 8 87 " --> pdb=" O PRO 8 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 543 removed outlier: 4.274A pdb=" N MET A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL A 539 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 595 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.579A pdb=" N ILE A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'C' and resid 58 through 63 removed outlier: 3.786A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 115 Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.907A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 removed outlier: 3.628A pdb=" N THR C 198 " --> pdb=" O ASN C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 195 through 198' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.912A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.103A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.593A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 543 removed outlier: 4.214A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.570A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.679A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.728A pdb=" N SER M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 64 removed outlier: 3.500A pdb=" N GLN Q 64 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 61 through 64' Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.836A pdb=" N THR Q 87 " --> pdb=" O PRO Q 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 82 removed outlier: 3.507A pdb=" N PHE R 82 " --> pdb=" O ARG R 79 " (cutoff:3.500A) Processing helix chain 'c' and resid 58 through 63 removed outlier: 3.803A pdb=" N THR c 63 " --> pdb=" O LYS c 59 " (cutoff:3.500A) Processing helix chain 'c' and resid 100 through 115 Processing helix chain 'c' and resid 122 through 126 removed outlier: 4.049A pdb=" N CYS c 126 " --> pdb=" O THR c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 195 through 198 removed outlier: 3.660A pdb=" N THR c 198 " --> pdb=" O ASN c 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 195 through 198' Processing helix chain 'c' and resid 335 through 350 Processing helix chain 'c' and resid 368 through 373 removed outlier: 3.865A pdb=" N THR c 372 " --> pdb=" O ASP c 368 " (cutoff:3.500A) Processing helix chain 'c' and resid 425 through 429 removed outlier: 4.151A pdb=" N ARG c 429 " --> pdb=" O MET c 426 " (cutoff:3.500A) Processing helix chain 'c' and resid 475 through 480 removed outlier: 3.617A pdb=" N TRP c 479 " --> pdb=" O MET c 475 " (cutoff:3.500A) Processing helix chain 'd' and resid 529 through 543 removed outlier: 4.287A pdb=" N MET d 535 " --> pdb=" O GLY d 531 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR d 536 " --> pdb=" O ALA d 532 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR d 538 " --> pdb=" O SER d 534 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL d 539 " --> pdb=" O MET d 535 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN d 540 " --> pdb=" O THR d 536 " (cutoff:3.500A) Processing helix chain 'd' and resid 570 through 595 Processing helix chain 'd' and resid 618 through 625 removed outlier: 3.503A pdb=" N ILE d 622 " --> pdb=" O ASN d 618 " (cutoff:3.500A) Processing helix chain 'd' and resid 627 through 635 removed outlier: 3.600A pdb=" N ILE d 635 " --> pdb=" O TRP d 631 " (cutoff:3.500A) Processing helix chain 'd' and resid 638 through 661 Processing helix chain 'h' and resid 61 through 64 Processing helix chain 'h' and resid 83 through 87 Processing helix chain 'l' and resid 79 through 83 removed outlier: 3.699A pdb=" N VAL l 83 " --> pdb=" O PRO l 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 83 through 87 removed outlier: 3.659A pdb=" N SER m 87 " --> pdb=" O ALA m 84 " (cutoff:3.500A) Processing helix chain 'q' and resid 61 through 64 removed outlier: 3.632A pdb=" N GLN q 64 " --> pdb=" O ARG q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 61 through 64' Processing helix chain 'q' and resid 83 through 87 removed outlier: 3.710A pdb=" N THR q 87 " --> pdb=" O PRO q 84 " (cutoff:3.500A) Processing helix chain 'r' and resid 78 through 82 Processing sheet with id=AA1, first strand: chain '2' and resid 495 through 499 removed outlier: 5.927A pdb=" N VAL A 608 " --> pdb=" O VAL 2 36 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N VAL 2 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR A 606 " --> pdb=" O VAL 2 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 45 through 47 removed outlier: 3.602A pdb=" N ILE 2 225 " --> pdb=" O VAL 2 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain '2' and resid 91 through 94 removed outlier: 3.627A pdb=" N GLU 2 91 " --> pdb=" O CYS 2 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain '2' and resid 202 through 203 removed outlier: 6.669A pdb=" N THR 2 202 " --> pdb=" O TYR 2 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 271 through 273 removed outlier: 7.583A pdb=" N GLN 2 293 " --> pdb=" O SER 2 334 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER 2 334 " --> pdb=" O GLN 2 293 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS 2 421 " --> pdb=" O PHE 2 382 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE 2 382 " --> pdb=" O LYS 2 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 271 through 273 removed outlier: 11.252A pdb=" N VAL 2 286 " --> pdb=" O THR 2 455 " (cutoff:3.500A) removed outlier: 10.788A pdb=" N THR 2 455 " --> pdb=" O VAL 2 286 " (cutoff:3.500A) removed outlier: 12.358A pdb=" N PHE 2 288 " --> pdb=" O ILE 2 453 " (cutoff:3.500A) removed outlier: 11.916A pdb=" N ILE 2 453 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 11.143A pdb=" N THR 2 290 " --> pdb=" O GLY 2 451 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY 2 451 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE 2 358 " --> pdb=" O GLU 2 466 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N PHE 2 468 " --> pdb=" O ILE 2 358 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG 2 360 " --> pdb=" O PHE 2 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '2' and resid 304 through 312 removed outlier: 6.780A pdb=" N GLN 2 315 " --> pdb=" O ILE 2 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 6 through 7 Processing sheet with id=AB2, first strand: chain '3' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain '3' and resid 57 through 59 removed outlier: 6.456A pdb=" N TRP 3 36 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY 3 50 " --> pdb=" O TRP 3 34 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP 3 34 " --> pdb=" O GLY 3 50 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL A 518 " --> pdb=" O ARG 3 95 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LYS 3 97 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '4' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain '4' and resid 10 through 12 removed outlier: 6.962A pdb=" N LEU 4 33 " --> pdb=" O TYR 4 49 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TYR 4 49 " --> pdb=" O LEU 4 33 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP 4 35 " --> pdb=" O LEU 4 47 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR 4 49 " --> pdb=" O THR 4 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '5' and resid 5 through 7 removed outlier: 3.833A pdb=" N GLN 5 5 " --> pdb=" O ASN 5 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '5' and resid 11 through 12 removed outlier: 3.525A pdb=" N THR 5 105 " --> pdb=" O TYR 5 90 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR 5 90 " --> pdb=" O THR 5 105 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP 5 34 " --> pdb=" O TYR 5 50 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR 5 50 " --> pdb=" O TRP 5 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP 5 36 " --> pdb=" O ILE 5 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '5' and resid 95 through 96 Processing sheet with id=AB9, first strand: chain '5' and resid 99 through 100A Processing sheet with id=AC1, first strand: chain '6' and resid 9 through 12 removed outlier: 6.155A pdb=" N VAL 6 11 " --> pdb=" O ILE 6 105 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP 6 35 " --> pdb=" O ILE 6 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '6' and resid 18 through 23 removed outlier: 3.859A pdb=" N ALA 6 71 " --> pdb=" O CYS 6 23 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '7' and resid 4 through 6 Processing sheet with id=AC4, first strand: chain '7' and resid 10 through 13 removed outlier: 6.452A pdb=" N TRP 7 34 " --> pdb=" O LEU 7 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '7' and resid 10 through 13 removed outlier: 3.640A pdb=" N GLN 7 89 " --> pdb=" O PHE 7 92 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '8' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain '8' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain '8' and resid 10 through 11 removed outlier: 3.598A pdb=" N GLY 8 49 " --> pdb=" O TRP 8 36 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG 8 38 " --> pdb=" O TRP 8 47 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N TRP 8 47 " --> pdb=" O ARG 8 38 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE 8 40 " --> pdb=" O PHE 8 45 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N PHE 8 45 " --> pdb=" O ILE 8 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '8' and resid 10 through 11 Processing sheet with id=AD1, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.862A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.617A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AD4, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.651A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AD6, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.664A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.490A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.809A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.547A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.772A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 518 through 519 removed outlier: 3.936A pdb=" N TYR H 99 " --> pdb=" O VAL D 518 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AE3, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AE4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.949A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 5 through 7 removed outlier: 3.997A pdb=" N GLN M 5 " --> pdb=" O ASN M 23 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.532A pdb=" N THR M 105 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR M 95 " --> pdb=" O TYR M 33 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR M 33 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 99 through 100A Processing sheet with id=AE9, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.123A pdb=" N VAL N 11 " --> pdb=" O ILE N 105 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 19 through 26 removed outlier: 3.925A pdb=" N ALA N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AF3, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'Q' and resid 10 through 11 removed outlier: 3.602A pdb=" N GLY Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE Q 40 " --> pdb=" O PHE Q 45 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N PHE Q 45 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 10 through 11 Processing sheet with id=AF6, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AF7, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.427A pdb=" N TRP R 34 " --> pdb=" O LEU R 46 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 10 through 13 removed outlier: 3.578A pdb=" N GLN R 89 " --> pdb=" O PHE R 92 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 495 through 499 removed outlier: 5.913A pdb=" N VAL d 608 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N VAL c 38 " --> pdb=" O THR d 606 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR d 606 " --> pdb=" O VAL c 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'c' and resid 45 through 47 removed outlier: 3.607A pdb=" N ILE c 225 " --> pdb=" O VAL c 245 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'c' and resid 53 through 56 Processing sheet with id=AG3, first strand: chain 'c' and resid 91 through 94 removed outlier: 3.675A pdb=" N GLU c 91 " --> pdb=" O CYS c 239 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'c' and resid 169 through 177 Processing sheet with id=AG5, first strand: chain 'c' and resid 202 through 203 removed outlier: 6.697A pdb=" N THR c 202 " --> pdb=" O TYR c 435 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'c' and resid 271 through 273 removed outlier: 7.410A pdb=" N GLN c 293 " --> pdb=" O SER c 334 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER c 334 " --> pdb=" O GLN c 293 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'c' and resid 271 through 273 removed outlier: 11.241A pdb=" N VAL c 286 " --> pdb=" O THR c 455 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N THR c 455 " --> pdb=" O VAL c 286 " (cutoff:3.500A) removed outlier: 12.239A pdb=" N PHE c 288 " --> pdb=" O ILE c 453 " (cutoff:3.500A) removed outlier: 11.783A pdb=" N ILE c 453 " --> pdb=" O PHE c 288 " (cutoff:3.500A) removed outlier: 11.056A pdb=" N THR c 290 " --> pdb=" O GLY c 451 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLY c 451 " --> pdb=" O THR c 290 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE c 358 " --> pdb=" O GLU c 466 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE c 468 " --> pdb=" O ILE c 358 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG c 360 " --> pdb=" O PHE c 468 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'c' and resid 304 through 312 removed outlier: 6.743A pdb=" N GLN c 315 " --> pdb=" O ILE c 309 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'd' and resid 518 through 519 removed outlier: 3.969A pdb=" N TYR h 99 " --> pdb=" O VAL d 518 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP h 34 " --> pdb=" O GLY h 50 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY h 50 " --> pdb=" O TRP h 34 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP h 36 " --> pdb=" O ILE h 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'h' and resid 11 through 12 Processing sheet with id=AH2, first strand: chain 'h' and resid 6 through 7 Processing sheet with id=AH3, first strand: chain 'l' and resid 4 through 7 Processing sheet with id=AH4, first strand: chain 'l' and resid 10 through 12 removed outlier: 6.954A pdb=" N LEU l 33 " --> pdb=" O TYR l 49 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR l 49 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP l 35 " --> pdb=" O LEU l 47 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'm' and resid 5 through 7 removed outlier: 3.980A pdb=" N GLN m 5 " --> pdb=" O ASN m 23 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.518A pdb=" N THR m 105 " --> pdb=" O TYR m 90 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR m 90 " --> pdb=" O THR m 105 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP m 34 " --> pdb=" O TYR m 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR m 50 " --> pdb=" O TRP m 34 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP m 36 " --> pdb=" O ILE m 48 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'm' and resid 99 through 100A Processing sheet with id=AH8, first strand: chain 'n' and resid 9 through 12 removed outlier: 6.198A pdb=" N VAL n 11 " --> pdb=" O ILE n 105 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP n 35 " --> pdb=" O ILE n 47 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'n' and resid 18 through 26 removed outlier: 3.956A pdb=" N ALA n 71 " --> pdb=" O CYS n 23 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'q' and resid 3 through 6 Processing sheet with id=AI2, first strand: chain 'q' and resid 3 through 6 Processing sheet with id=AI3, first strand: chain 'q' and resid 10 through 11 removed outlier: 3.586A pdb=" N GLY q 49 " --> pdb=" O TRP q 36 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ARG q 38 " --> pdb=" O TRP q 47 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N TRP q 47 " --> pdb=" O ARG q 38 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE q 40 " --> pdb=" O PHE q 45 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N PHE q 45 " --> pdb=" O ILE q 40 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'q' and resid 10 through 11 Processing sheet with id=AI5, first strand: chain 'r' and resid 4 through 6 Processing sheet with id=AI6, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.495A pdb=" N TRP r 34 " --> pdb=" O LEU r 46 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'r' and resid 10 through 13 removed outlier: 3.633A pdb=" N GLN r 89 " --> pdb=" O PHE r 92 " (cutoff:3.500A) 1124 hydrogen bonds defined for protein. 2832 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.73 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9967 1.34 - 1.46: 8344 1.46 - 1.58: 14064 1.58 - 1.70: 1 1.70 - 1.82: 222 Bond restraints: 32598 Sorted by residual: bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.32e+00 bond pdb=" C1 MANAA 4 " pdb=" C2 MANAA 4 " ideal model delta sigma weight residual 1.526 1.583 -0.057 2.00e-02 2.50e+03 8.08e+00 bond pdb=" C1 MAN T 5 " pdb=" O5 MAN T 5 " ideal model delta sigma weight residual 1.399 1.456 -0.057 2.00e-02 2.50e+03 8.06e+00 bond pdb=" C1 NAG 0 2 " pdb=" O5 NAG 0 2 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C1 NAG i 2 " pdb=" O5 NAG i 2 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.92e+00 ... (remaining 32593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 42386 2.00 - 4.00: 1568 4.00 - 6.01: 229 6.01 - 8.01: 92 8.01 - 10.01: 17 Bond angle restraints: 44292 Sorted by residual: angle pdb=" N PHE 8 100D" pdb=" CA PHE 8 100D" pdb=" C PHE 8 100D" ideal model delta sigma weight residual 109.81 119.66 -9.85 2.21e+00 2.05e-01 1.99e+01 angle pdb=" N PHE Q 100D" pdb=" CA PHE Q 100D" pdb=" C PHE Q 100D" ideal model delta sigma weight residual 109.81 119.48 -9.67 2.21e+00 2.05e-01 1.92e+01 angle pdb=" N PHE q 100D" pdb=" CA PHE q 100D" pdb=" C PHE q 100D" ideal model delta sigma weight residual 109.81 118.81 -9.00 2.21e+00 2.05e-01 1.66e+01 angle pdb=" C ILE 4 29 " pdb=" N ASP 4 30 " pdb=" CA ASP 4 30 " ideal model delta sigma weight residual 121.54 129.10 -7.56 1.91e+00 2.74e-01 1.57e+01 angle pdb=" C ILE l 29 " pdb=" N ASP l 30 " pdb=" CA ASP l 30 " ideal model delta sigma weight residual 121.54 128.95 -7.41 1.91e+00 2.74e-01 1.51e+01 ... (remaining 44287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 16696 17.01 - 34.01: 1237 34.01 - 51.02: 246 51.02 - 68.03: 70 68.03 - 85.04: 21 Dihedral angle restraints: 18270 sinusoidal: 7245 harmonic: 11025 Sorted by residual: dihedral pdb=" CA GLN 7 89 " pdb=" C GLN 7 89 " pdb=" N PHE 7 90 " pdb=" CA PHE 7 90 " ideal model delta harmonic sigma weight residual -180.00 -133.96 -46.04 0 5.00e+00 4.00e-02 8.48e+01 dihedral pdb=" CA GLN r 89 " pdb=" C GLN r 89 " pdb=" N PHE r 90 " pdb=" CA PHE r 90 " ideal model delta harmonic sigma weight residual -180.00 -134.52 -45.48 0 5.00e+00 4.00e-02 8.27e+01 dihedral pdb=" CA GLN R 89 " pdb=" C GLN R 89 " pdb=" N PHE R 90 " pdb=" CA PHE R 90 " ideal model delta harmonic sigma weight residual -180.00 -135.68 -44.32 0 5.00e+00 4.00e-02 7.86e+01 ... (remaining 18267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 4368 0.071 - 0.143: 864 0.143 - 0.214: 52 0.214 - 0.286: 20 0.286 - 0.357: 18 Chirality restraints: 5322 Sorted by residual: chirality pdb=" C1 NAG v 1 " pdb=" ND2 ASN c 234 " pdb=" C2 NAG v 1 " pdb=" O5 NAG v 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.60 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C5 BMA w 3 " pdb=" C4 BMA w 3 " pdb=" C6 BMA w 3 " pdb=" O5 BMA w 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.60 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 5319 not shown) Planarity restraints: 5499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE Q 100D" -0.048 5.00e-02 4.00e+02 7.27e-02 8.47e+00 pdb=" N PRO Q 100E" 0.126 5.00e-02 4.00e+02 pdb=" CA PRO Q 100E" -0.037 5.00e-02 4.00e+02 pdb=" CD PRO Q 100E" -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE q 100D" 0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO q 100E" -0.125 5.00e-02 4.00e+02 pdb=" CA PRO q 100E" 0.036 5.00e-02 4.00e+02 pdb=" CD PRO q 100E" 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE 8 100D" 0.046 5.00e-02 4.00e+02 6.91e-02 7.65e+00 pdb=" N PRO 8 100E" -0.120 5.00e-02 4.00e+02 pdb=" CA PRO 8 100E" 0.035 5.00e-02 4.00e+02 pdb=" CD PRO 8 100E" 0.039 5.00e-02 4.00e+02 ... (remaining 5496 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 10252 2.83 - 3.35: 26578 3.35 - 3.87: 53550 3.87 - 4.38: 58404 4.38 - 4.90: 100651 Nonbonded interactions: 249435 Sorted by model distance: nonbonded pdb=" O ASP 7 81 " pdb=" OH TYR 7 85 " model vdw 2.314 3.040 nonbonded pdb=" N ASN c 195 " pdb=" OD1 ASN c 195 " model vdw 2.317 3.120 nonbonded pdb=" OE1 GLN 7 6 " pdb=" OG SER 7 97 " model vdw 2.323 3.040 nonbonded pdb=" N ASP 8 76E" pdb=" OD1 ASP 8 76E" model vdw 2.325 3.120 nonbonded pdb=" OG SER m 7 " pdb=" OG1 THR m 21 " model vdw 2.333 3.040 ... (remaining 249430 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: 0.06 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'AA' selection = chain 'E' selection = chain 'S' selection = chain 'V' selection = chain 'X' selection = chain 'i' selection = chain 'o' selection = chain 's' } ncs_group { reference = chain '1' selection = chain 'T' selection = chain 'j' } ncs_group { reference = chain '2' selection = chain 'C' selection = chain 'c' } ncs_group { reference = chain '3' selection = chain 'H' selection = chain 'h' } ncs_group { reference = chain '4' selection = chain 'L' selection = chain 'l' } ncs_group { reference = chain '5' selection = chain 'M' selection = chain 'm' } ncs_group { reference = chain '6' selection = chain 'N' selection = chain 'n' } ncs_group { reference = chain '7' selection = chain 'R' selection = chain 'r' } ncs_group { reference = chain '8' selection = chain 'Q' selection = chain 'q' } ncs_group { reference = chain '9' selection = chain 'B' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'O' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'k' selection = chain 'p' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'J' selection = chain 'b' selection = chain 'w' } ncs_group { reference = chain 'P' selection = chain 'g' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.920 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: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 31.340 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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 0.076 32778 Z= 0.300 Angle : 0.977 12.546 44787 Z= 0.484 Chirality : 0.058 0.357 5322 Planarity : 0.006 0.073 5454 Dihedral : 13.083 85.036 11067 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 7.06 % Allowed : 6.94 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.12), residues: 3786 helix: -1.82 (0.21), residues: 387 sheet: -1.65 (0.13), residues: 1317 loop : -2.34 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG q 94 TYR 0.018 0.002 TYR 3 99 PHE 0.025 0.002 PHE 2 288 TRP 0.018 0.002 TRP D 571 HIS 0.011 0.002 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.30 (32598) covalent geometry : angle 0.92752 / 0.47 (44292) SS BOND : bond 0.00292 / 0.19 ( 45) SS BOND : angle 0.91375 / 0.61 ( 90) hydrogen bonds : bond 0.14912 / 9.45 ( 1043) hydrogen bonds : angle 7.26409 / 5.02 ( 2832) link_ALPHA1-2 : bond 0.00880 / 0.53 ( 6) link_ALPHA1-2 : angle 2.34970 / 1.34 ( 18) link_ALPHA1-3 : bond 0.00550 / 0.37 ( 18) link_ALPHA1-3 : angle 2.22686 / 1.52 ( 54) link_ALPHA1-6 : bond 0.00336 / 0.21 ( 9) link_ALPHA1-6 : angle 1.92008 / 1.14 ( 27) link_BETA1-4 : bond 0.00653 / 0.40 ( 57) link_BETA1-4 : angle 3.81074 / 2.70 ( 171) link_NAG-ASN : bond 0.00900 / 0.55 ( 45) link_NAG-ASN : angle 3.47795 / 2.42 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 898 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 83 GLU cc_start: 0.8793 (pt0) cc_final: 0.8560 (pm20) REVERT: 2 100 MET cc_start: 0.9182 (ptt) cc_final: 0.8916 (ptt) REVERT: 2 138 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8304 (mt) REVERT: 2 207 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8876 (tppt) REVERT: 2 260 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8031 (pp) REVERT: 2 321 ASP cc_start: 0.8596 (t0) cc_final: 0.8333 (t0) REVERT: 2 425 ASN cc_start: 0.8629 (t0) cc_final: 0.8117 (t0) REVERT: 2 443 ILE cc_start: 0.8809 (mm) cc_final: 0.8331 (tt) REVERT: 2 479 TRP cc_start: 0.9279 (m100) cc_final: 0.9009 (m100) REVERT: 2 492 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8450 (mp0) REVERT: 3 23 GLU cc_start: 0.9133 (tp30) cc_final: 0.8894 (tp30) REVERT: 3 53 ASN cc_start: 0.8554 (m-40) cc_final: 0.8240 (p0) REVERT: 3 55 GLU cc_start: 0.6060 (mm-30) cc_final: 0.5625 (mm-30) REVERT: 3 68 ILE cc_start: 0.8598 (mm) cc_final: 0.8361 (mm) REVERT: 3 95 ARG cc_start: 0.4762 (OUTLIER) cc_final: 0.4420 (ttp-170) REVERT: 6 78 VAL cc_start: 0.9085 (m) cc_final: 0.8760 (p) REVERT: 6 85 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8537 (t0) REVERT: 6 105 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6914 (tt) REVERT: 6 106 VAL cc_start: 0.7400 (OUTLIER) cc_final: 0.6666 (t) REVERT: 7 1 GLU cc_start: 0.7928 (pt0) cc_final: 0.7341 (pm20) REVERT: 7 33 THR cc_start: 0.9215 (m) cc_final: 0.8912 (m) REVERT: 7 48 TYR cc_start: 0.8717 (p90) cc_final: 0.8300 (p90) REVERT: 7 77 LEU cc_start: 0.9303 (mt) cc_final: 0.9066 (tp) REVERT: 7 78 ASP cc_start: 0.9284 (t70) cc_final: 0.9013 (t70) REVERT: 8 30 ARG cc_start: 0.9090 (mtt90) cc_final: 0.8741 (mtt90) REVERT: 8 47 TRP cc_start: 0.8940 (t60) cc_final: 0.8297 (t60) REVERT: 8 48 ILE cc_start: 0.8464 (mt) cc_final: 0.7127 (mp) REVERT: 8 72 GLN cc_start: 0.9521 (tt0) cc_final: 0.9010 (tm-30) REVERT: 8 89 GLU cc_start: 0.7624 (tt0) cc_final: 0.7351 (tt0) REVERT: 8 100 TYR cc_start: 0.8448 (m-80) cc_final: 0.8092 (m-10) REVERT: A 539 VAL cc_start: 0.9490 (OUTLIER) cc_final: 0.9268 (t) REVERT: A 588 ARG cc_start: 0.9100 (mtt180) cc_final: 0.8538 (ttm110) REVERT: A 589 ASP cc_start: 0.8728 (m-30) cc_final: 0.8500 (m-30) REVERT: A 592 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8766 (tt) REVERT: C 45 TRP cc_start: 0.8799 (p90) cc_final: 0.8596 (p90) REVERT: C 83 GLU cc_start: 0.8882 (pt0) cc_final: 0.8514 (pm20) REVERT: C 100 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8555 (ptt) REVERT: C 138 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8494 (tt) REVERT: C 207 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8847 (tptp) REVERT: C 279 ASN cc_start: 0.9273 (t0) cc_final: 0.8932 (t0) REVERT: C 492 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8634 (mp0) REVERT: D 592 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8665 (tp) REVERT: D 601 LYS cc_start: 0.8081 (mtpp) cc_final: 0.7801 (mtpt) REVERT: D 622 ILE cc_start: 0.9621 (pt) cc_final: 0.9384 (pt) REVERT: D 638 TYR cc_start: 0.8996 (OUTLIER) cc_final: 0.8506 (m-80) REVERT: H 23 GLU cc_start: 0.9142 (tp30) cc_final: 0.8935 (tp30) REVERT: H 53 ASN cc_start: 0.8562 (m-40) cc_final: 0.8200 (p0) REVERT: M 90 TYR cc_start: 0.8660 (m-10) cc_final: 0.8005 (m-10) REVERT: M 100 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7883 (mt-10) REVERT: M 105 THR cc_start: 0.7356 (m) cc_final: 0.7134 (p) REVERT: N 85 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8403 (t0) REVERT: N 106 VAL cc_start: 0.7466 (OUTLIER) cc_final: 0.6679 (p) REVERT: Q 5 VAL cc_start: 0.9241 (t) cc_final: 0.8855 (p) REVERT: Q 30 ARG cc_start: 0.9134 (mtt90) cc_final: 0.8788 (mtt90) REVERT: Q 72 GLN cc_start: 0.9397 (tt0) cc_final: 0.9004 (tm-30) REVERT: Q 73 LEU cc_start: 0.8308 (mt) cc_final: 0.7733 (mt) REVERT: Q 89 GLU cc_start: 0.7607 (tt0) cc_final: 0.7291 (tt0) REVERT: Q 108 VAL cc_start: 0.9623 (t) cc_final: 0.9360 (p) REVERT: R 33 THR cc_start: 0.9147 (m) cc_final: 0.8751 (m) REVERT: R 35 TYR cc_start: 0.8706 (m-10) cc_final: 0.8442 (m-80) REVERT: R 46 LEU cc_start: 0.9417 (mt) cc_final: 0.9074 (mt) REVERT: R 77 LEU cc_start: 0.9052 (mt) cc_final: 0.8720 (tp) REVERT: c 100 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8061 (ppp) REVERT: c 256 SER cc_start: 0.9264 (p) cc_final: 0.8966 (t) REVERT: c 321 ASP cc_start: 0.8716 (t0) cc_final: 0.8343 (t0) REVERT: c 334 SER cc_start: 0.8655 (OUTLIER) cc_final: 0.8126 (p) REVERT: c 425 ASN cc_start: 0.8732 (t0) cc_final: 0.8102 (t0) REVERT: c 475 MET cc_start: 0.8856 (mmm) cc_final: 0.8534 (mmm) REVERT: c 479 TRP cc_start: 0.9172 (m100) cc_final: 0.8799 (m100) REVERT: c 491 ILE cc_start: 0.9341 (mm) cc_final: 0.8893 (mp) REVERT: c 492 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8511 (mm-30) REVERT: d 539 VAL cc_start: 0.9517 (OUTLIER) cc_final: 0.9158 (t) REVERT: d 579 ARG cc_start: 0.8787 (ttp-170) cc_final: 0.8548 (ttp-170) REVERT: d 581 LEU cc_start: 0.9565 (tp) cc_final: 0.9364 (tt) REVERT: d 588 ARG cc_start: 0.9047 (mtt180) cc_final: 0.8755 (ttm-80) REVERT: d 592 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8766 (tt) REVERT: d 593 LEU cc_start: 0.9213 (tp) cc_final: 0.9008 (tp) REVERT: d 596 TRP cc_start: 0.8843 (m-10) cc_final: 0.8120 (m-10) REVERT: d 619 LEU cc_start: 0.9286 (tp) cc_final: 0.9083 (mm) REVERT: d 638 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8641 (m-80) REVERT: h 55 GLU cc_start: 0.5439 (mm-30) cc_final: 0.4997 (mm-30) REVERT: h 95 ARG cc_start: 0.4065 (OUTLIER) cc_final: 0.3816 (ttp-170) REVERT: m 90 TYR cc_start: 0.8555 (m-10) cc_final: 0.8043 (m-10) REVERT: m 100 LYS cc_start: 0.9085 (mptt) cc_final: 0.8795 (tmtt) REVERT: n 13 VAL cc_start: 0.8772 (OUTLIER) cc_final: 0.8541 (t) REVERT: n 78 VAL cc_start: 0.8752 (m) cc_final: 0.8432 (p) REVERT: n 85 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8050 (t0) REVERT: q 18 VAL cc_start: 0.9449 (OUTLIER) cc_final: 0.9129 (m) REVERT: q 28 ASN cc_start: 0.8589 (t0) cc_final: 0.8366 (t0) REVERT: q 42 ASP cc_start: 0.8456 (m-30) cc_final: 0.8135 (p0) REVERT: q 69 MET cc_start: 0.9302 (mtt) cc_final: 0.9080 (mtm) REVERT: q 72 GLN cc_start: 0.9430 (tt0) cc_final: 0.9137 (tm-30) REVERT: q 73 LEU cc_start: 0.8520 (mt) cc_final: 0.8157 (mt) REVERT: q 82 PHE cc_start: 0.8480 (t80) cc_final: 0.8146 (t80) REVERT: r 27 GLN cc_start: 0.8774 (mt0) cc_final: 0.8530 (mp10) REVERT: r 45 LEU cc_start: 0.9285 (tt) cc_final: 0.9003 (tt) REVERT: r 57 VAL cc_start: 0.8888 (t) cc_final: 0.8430 (t) REVERT: r 77 LEU cc_start: 0.9216 (mt) cc_final: 0.8935 (tp) outliers start: 236 outliers final: 65 residues processed: 1064 average time/residue: 0.2215 time to fit residues: 361.6319 Evaluate side-chains 561 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 471 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 72 HIS 2 80 ASN 2 315 GLN ** 2 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 377 ASN 2 448 ASN 4 89 GLN ** 4 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 23 ASN 5 97 HIS 7 27 GLN 8 6 GLN 8 101 GLN A 611 ASN A 658 GLN C 72 HIS C 80 ASN C 293 GLN C 315 GLN ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN D 577 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN L 89 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN Q 35 HIS Q 101 GLN R 27 GLN c 72 HIS c 80 ASN c 315 GLN ** c 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 377 ASN ** d 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 611 ASN d 658 GLN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 89 GLN l 90 GLN m 23 ASN q 6 GLN q 101 GLN r 30 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.093048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.066601 restraints weight = 122814.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.069071 restraints weight = 63815.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.070693 restraints weight = 41506.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.071749 restraints weight = 31179.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.072288 restraints weight = 25839.391| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32778 Z= 0.186 Angle : 0.756 13.254 44787 Z= 0.373 Chirality : 0.048 0.266 5322 Planarity : 0.007 0.160 5454 Dihedral : 5.589 32.227 4149 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.30 % Allowed : 2.99 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.13), residues: 3786 helix: -0.10 (0.25), residues: 393 sheet: -1.09 (0.13), residues: 1272 loop : -1.84 (0.12), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG 4 61 TYR 0.022 0.002 TYR Q 102 PHE 0.026 0.002 PHE Q 100D TRP 0.018 0.002 TRP Q 100F HIS 0.008 0.001 HIS c 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (32598) covalent geometry : angle 0.72148 / 0.37 (44292) SS BOND : bond 0.00393 / 0.22 ( 45) SS BOND : angle 1.89340 / 1.34 ( 90) hydrogen bonds : bond 0.04048 / 2.69 ( 1043) hydrogen bonds : angle 6.11079 / 4.21 ( 2832) link_ALPHA1-2 : bond 0.00930 / 0.53 ( 6) link_ALPHA1-2 : angle 2.11110 / 1.20 ( 18) link_ALPHA1-3 : bond 0.00666 / 0.45 ( 18) link_ALPHA1-3 : angle 1.84800 / 1.22 ( 54) link_ALPHA1-6 : bond 0.00310 / 0.19 ( 9) link_ALPHA1-6 : angle 1.55109 / 1.02 ( 27) link_BETA1-4 : bond 0.00399 / 0.25 ( 57) link_BETA1-4 : angle 2.47706 / 1.74 ( 171) link_NAG-ASN : bond 0.00506 / 0.31 ( 45) link_NAG-ASN : angle 2.46505 / 1.71 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 627 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 83 GLU cc_start: 0.8739 (pt0) cc_final: 0.8290 (pm20) REVERT: 2 95 MET cc_start: 0.8595 (pmm) cc_final: 0.8209 (pmm) REVERT: 2 190 GLU cc_start: 0.8454 (pt0) cc_final: 0.8234 (pm20) REVERT: 2 321 ASP cc_start: 0.8052 (t0) cc_final: 0.7819 (t0) REVERT: 2 425 ASN cc_start: 0.8703 (t0) cc_final: 0.8317 (t0) REVERT: 2 492 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8553 (mm-30) REVERT: 3 23 GLU cc_start: 0.9145 (tp30) cc_final: 0.8900 (tp30) REVERT: 3 51 MET cc_start: 0.2878 (ttp) cc_final: 0.1905 (ttm) REVERT: 3 53 ASN cc_start: 0.8545 (m-40) cc_final: 0.8240 (p0) REVERT: 3 55 GLU cc_start: 0.6227 (mm-30) cc_final: 0.5634 (mm-30) REVERT: 3 81 ARG cc_start: 0.8743 (ttp-110) cc_final: 0.8006 (mtt90) REVERT: 4 4 MET cc_start: 0.2755 (mmt) cc_final: 0.1888 (mtp) REVERT: 7 33 THR cc_start: 0.9176 (m) cc_final: 0.8855 (p) REVERT: 7 48 TYR cc_start: 0.8703 (p90) cc_final: 0.8387 (p90) REVERT: 7 70 PHE cc_start: 0.8442 (m-10) cc_final: 0.8166 (m-10) REVERT: 7 77 LEU cc_start: 0.9325 (mt) cc_final: 0.9112 (tp) REVERT: 7 80 GLU cc_start: 0.8661 (pp20) cc_final: 0.8450 (mm-30) REVERT: 7 81 ASP cc_start: 0.9434 (m-30) cc_final: 0.8986 (m-30) REVERT: 8 27 TYR cc_start: 0.8432 (p90) cc_final: 0.8146 (p90) REVERT: 8 47 TRP cc_start: 0.8949 (t60) cc_final: 0.8332 (t60) REVERT: 8 48 ILE cc_start: 0.8429 (mt) cc_final: 0.7447 (mp) REVERT: 8 52 LYS cc_start: 0.9284 (mtmm) cc_final: 0.8550 (mtmm) REVERT: 8 72 GLN cc_start: 0.9390 (tt0) cc_final: 0.9113 (tp40) REVERT: 8 80 MET cc_start: 0.8287 (tmm) cc_final: 0.7955 (tmm) REVERT: 8 100 TYR cc_start: 0.8433 (m-80) cc_final: 0.8083 (m-10) REVERT: A 588 ARG cc_start: 0.9047 (mtt180) cc_final: 0.8598 (ttm110) REVERT: A 589 ASP cc_start: 0.8676 (m-30) cc_final: 0.8409 (m-30) REVERT: A 591 GLN cc_start: 0.9380 (tm-30) cc_final: 0.8902 (tm-30) REVERT: A 632 ASP cc_start: 0.8862 (t0) cc_final: 0.8609 (t70) REVERT: C 45 TRP cc_start: 0.8973 (p90) cc_final: 0.8440 (p90) REVERT: C 83 GLU cc_start: 0.8868 (pt0) cc_final: 0.8357 (pm20) REVERT: C 95 MET cc_start: 0.8768 (pmm) cc_final: 0.8352 (pmm) REVERT: C 492 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8131 (tm-30) REVERT: D 601 LYS cc_start: 0.8057 (mtpp) cc_final: 0.7771 (mtpt) REVERT: D 647 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8276 (mt-10) REVERT: H 23 GLU cc_start: 0.9120 (tp30) cc_final: 0.8894 (tp30) REVERT: H 51 MET cc_start: 0.2694 (ttm) cc_final: 0.2012 (ttm) REVERT: H 53 ASN cc_start: 0.8454 (m-40) cc_final: 0.8086 (p0) REVERT: H 55 GLU cc_start: 0.5701 (mm-30) cc_final: 0.5448 (mm-30) REVERT: H 86 ASP cc_start: 0.3410 (m-30) cc_final: 0.2953 (m-30) REVERT: L 4 MET cc_start: 0.2362 (mmt) cc_final: 0.1081 (mtp) REVERT: L 92 PHE cc_start: 0.8074 (t80) cc_final: 0.7842 (t80) REVERT: M 105 THR cc_start: 0.7985 (m) cc_final: 0.7643 (p) REVERT: Q 52 LYS cc_start: 0.9312 (mtmm) cc_final: 0.8682 (mtmm) REVERT: Q 69 MET cc_start: 0.9318 (mtt) cc_final: 0.9111 (mtp) REVERT: Q 80 MET cc_start: 0.8494 (tmm) cc_final: 0.8229 (tmm) REVERT: R 33 THR cc_start: 0.9027 (m) cc_final: 0.8817 (m) REVERT: R 45 LEU cc_start: 0.9075 (mt) cc_final: 0.8804 (mt) REVERT: R 53 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.8105 (ttm110) REVERT: c 83 GLU cc_start: 0.8732 (pt0) cc_final: 0.8456 (pm20) REVERT: c 100 MET cc_start: 0.8925 (ptt) cc_final: 0.8585 (ptp) REVERT: c 321 ASP cc_start: 0.8267 (t0) cc_final: 0.7761 (t0) REVERT: c 425 ASN cc_start: 0.8740 (t0) cc_final: 0.8196 (t0) REVERT: c 491 ILE cc_start: 0.9327 (mm) cc_final: 0.8956 (mp) REVERT: c 492 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8361 (mp0) REVERT: d 542 ARG cc_start: 0.8799 (ttp-110) cc_final: 0.8481 (ptm160) REVERT: d 588 ARG cc_start: 0.9045 (mtt180) cc_final: 0.8771 (ttm-80) REVERT: d 589 ASP cc_start: 0.8773 (m-30) cc_final: 0.8538 (m-30) REVERT: d 591 GLN cc_start: 0.9307 (tm-30) cc_final: 0.9003 (tm-30) REVERT: d 655 LYS cc_start: 0.9587 (mmmm) cc_final: 0.9015 (pttp) REVERT: h 51 MET cc_start: 0.4012 (ttp) cc_final: 0.2733 (ttm) REVERT: h 55 GLU cc_start: 0.5476 (mm-30) cc_final: 0.5021 (mm-30) REVERT: h 97 LYS cc_start: 0.9059 (mtmt) cc_final: 0.8849 (mtpp) REVERT: l 4 MET cc_start: 0.3263 (mmt) cc_final: 0.2554 (mtp) REVERT: l 32 ASP cc_start: 0.5537 (p0) cc_final: 0.4617 (p0) REVERT: l 62 PHE cc_start: 0.2162 (m-80) cc_final: 0.1918 (m-80) REVERT: l 82 ASP cc_start: 0.5164 (p0) cc_final: 0.2725 (p0) REVERT: l 96 LEU cc_start: 0.8047 (mm) cc_final: 0.7798 (tp) REVERT: m 90 TYR cc_start: 0.8393 (m-10) cc_final: 0.8123 (m-10) REVERT: m 100 LYS cc_start: 0.9067 (mptt) cc_final: 0.8775 (tmtt) REVERT: n 85 ASP cc_start: 0.8544 (m-30) cc_final: 0.8204 (t0) REVERT: q 28 ASN cc_start: 0.8828 (t0) cc_final: 0.8411 (t0) REVERT: q 52 LYS cc_start: 0.9261 (mtmm) cc_final: 0.8456 (mtmm) REVERT: q 82 PHE cc_start: 0.8379 (t80) cc_final: 0.8036 (t80) REVERT: q 105 GLN cc_start: 0.9019 (pp30) cc_final: 0.8750 (pp30) REVERT: r 33 THR cc_start: 0.9084 (m) cc_final: 0.8828 (p) REVERT: r 59 ASP cc_start: 0.8936 (t0) cc_final: 0.8645 (t0) REVERT: r 77 LEU cc_start: 0.9306 (mt) cc_final: 0.9000 (tp) outliers start: 10 outliers final: 2 residues processed: 636 average time/residue: 0.2130 time to fit residues: 211.3029 Evaluate side-chains 435 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 433 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 159 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 337 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 192 optimal weight: 20.0000 chunk 298 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 274 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 85 HIS ** 2 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 352 HIS ** 4 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 42 GLN 7 89 GLN C 80 ASN C 85 HIS C 352 HIS D 656 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 HIS Q 3 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 80 ASN c 85 HIS c 98 ASN c 99 ASN c 103 GLN c 352 HIS ** d 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 656 ASN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 97 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.088296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.061603 restraints weight = 128014.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.063789 restraints weight = 69055.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.065196 restraints weight = 46312.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.066163 restraints weight = 35797.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.066742 restraints weight = 30162.725| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 32778 Z= 0.295 Angle : 0.848 15.886 44787 Z= 0.413 Chirality : 0.049 0.278 5322 Planarity : 0.006 0.118 5454 Dihedral : 5.733 30.101 4149 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.12 % Allowed : 4.70 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: -1.90 (0.13), residues: 3786 helix: 0.30 (0.26), residues: 381 sheet: -1.04 (0.13), residues: 1290 loop : -1.72 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 4 61 TYR 0.021 0.002 TYR 3 100 PHE 0.023 0.002 PHE 2 353 TRP 0.033 0.002 TRP Q 100F HIS 0.006 0.001 HIS c 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.29 (32598) covalent geometry : angle 0.81340 / 0.41 (44292) SS BOND : bond 0.00523 / 0.29 ( 45) SS BOND : angle 2.00475 / 1.40 ( 90) hydrogen bonds : bond 0.04414 / 2.93 ( 1043) hydrogen bonds : angle 6.14912 / 4.24 ( 2832) link_ALPHA1-2 : bond 0.01170 / 0.71 ( 6) link_ALPHA1-2 : angle 2.21022 / 1.27 ( 18) link_ALPHA1-3 : bond 0.00525 / 0.35 ( 18) link_ALPHA1-3 : angle 2.06682 / 1.35 ( 54) link_ALPHA1-6 : bond 0.00376 / 0.24 ( 9) link_ALPHA1-6 : angle 1.56436 / 1.00 ( 27) link_BETA1-4 : bond 0.00422 / 0.29 ( 57) link_BETA1-4 : angle 2.61194 / 1.83 ( 171) link_NAG-ASN : bond 0.00893 / 0.52 ( 45) link_NAG-ASN : angle 2.74557 / 1.86 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 528 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 45 TRP cc_start: 0.9078 (p90) cc_final: 0.8598 (p90) REVERT: 2 52 LEU cc_start: 0.9502 (mt) cc_final: 0.9282 (mm) REVERT: 2 83 GLU cc_start: 0.8926 (pt0) cc_final: 0.8423 (pm20) REVERT: 2 100 MET cc_start: 0.9393 (ptp) cc_final: 0.8948 (ptp) REVERT: 2 119 CYS cc_start: 0.6647 (m) cc_final: 0.6370 (m) REVERT: 2 232 LYS cc_start: 0.9004 (mppt) cc_final: 0.8742 (mppt) REVERT: 2 321 ASP cc_start: 0.8253 (t0) cc_final: 0.8046 (t0) REVERT: 2 492 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8498 (mp0) REVERT: 3 23 GLU cc_start: 0.9239 (tp30) cc_final: 0.9010 (tp30) REVERT: 3 51 MET cc_start: 0.3077 (ttp) cc_final: 0.1001 (ttm) REVERT: 3 53 ASN cc_start: 0.8554 (m-40) cc_final: 0.8154 (p0) REVERT: 3 55 GLU cc_start: 0.6181 (mm-30) cc_final: 0.5456 (mm-30) REVERT: 4 4 MET cc_start: 0.3814 (mmt) cc_final: 0.3149 (mtp) REVERT: 7 1 GLU cc_start: 0.8218 (pm20) cc_final: 0.8004 (pm20) REVERT: 7 33 THR cc_start: 0.9141 (m) cc_final: 0.8928 (m) REVERT: 7 48 TYR cc_start: 0.8892 (p90) cc_final: 0.8597 (p90) REVERT: 7 77 LEU cc_start: 0.9348 (mt) cc_final: 0.9140 (tp) REVERT: 8 32 TYR cc_start: 0.8986 (m-80) cc_final: 0.8601 (m-10) REVERT: 8 72 GLN cc_start: 0.9417 (tt0) cc_final: 0.9114 (tp40) REVERT: 8 80 MET cc_start: 0.8424 (tmm) cc_final: 0.8213 (tmm) REVERT: A 588 ARG cc_start: 0.9090 (mtt180) cc_final: 0.8628 (ttm110) REVERT: A 589 ASP cc_start: 0.8801 (m-30) cc_final: 0.8560 (m-30) REVERT: A 591 GLN cc_start: 0.9433 (tm-30) cc_final: 0.9026 (tm-30) REVERT: A 632 ASP cc_start: 0.8965 (t0) cc_final: 0.8757 (t70) REVERT: C 45 TRP cc_start: 0.9109 (p90) cc_final: 0.8310 (p90) REVERT: C 83 GLU cc_start: 0.8984 (pt0) cc_final: 0.8511 (pm20) REVERT: C 95 MET cc_start: 0.8969 (pmm) cc_final: 0.8517 (pmm) REVERT: C 161 MET cc_start: 0.9278 (tpp) cc_final: 0.8577 (tpp) REVERT: C 492 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8618 (mp0) REVERT: H 51 MET cc_start: 0.2890 (ttm) cc_final: 0.2153 (ttm) REVERT: H 53 ASN cc_start: 0.8245 (m-40) cc_final: 0.7888 (p0) REVERT: H 55 GLU cc_start: 0.5617 (mm-30) cc_final: 0.5132 (mm-30) REVERT: L 4 MET cc_start: 0.3218 (mmt) cc_final: 0.2556 (mtp) REVERT: L 32 ASP cc_start: 0.6874 (m-30) cc_final: 0.6652 (m-30) REVERT: L 92 PHE cc_start: 0.8229 (t80) cc_final: 0.7953 (t80) REVERT: M 105 THR cc_start: 0.7924 (m) cc_final: 0.7632 (p) REVERT: N 26 GLU cc_start: 0.8835 (tp30) cc_final: 0.8602 (tp30) REVERT: N 28 LEU cc_start: 0.8933 (mt) cc_final: 0.8408 (mt) REVERT: N 95 ARG cc_start: 0.9284 (tpp80) cc_final: 0.9052 (tpp-160) REVERT: Q 19 LYS cc_start: 0.8791 (tptm) cc_final: 0.8307 (tptm) REVERT: R 33 THR cc_start: 0.9036 (m) cc_final: 0.8769 (m) REVERT: R 45 LEU cc_start: 0.9118 (mt) cc_final: 0.8840 (mt) REVERT: R 53 ARG cc_start: 0.8646 (mtm-85) cc_final: 0.8063 (ttm110) REVERT: R 78 ASP cc_start: 0.9122 (t70) cc_final: 0.8891 (t70) REVERT: c 83 GLU cc_start: 0.8793 (pt0) cc_final: 0.8382 (pm20) REVERT: c 100 MET cc_start: 0.9312 (ptt) cc_final: 0.8433 (ppp) REVERT: c 104 MET cc_start: 0.9235 (tmm) cc_final: 0.8829 (tmm) REVERT: c 122 LEU cc_start: 0.9610 (mp) cc_final: 0.9402 (mm) REVERT: c 123 THR cc_start: 0.9258 (p) cc_final: 0.8949 (t) REVERT: c 321 ASP cc_start: 0.8527 (t0) cc_final: 0.8035 (t0) REVERT: c 425 ASN cc_start: 0.8986 (t0) cc_final: 0.8479 (t0) REVERT: c 491 ILE cc_start: 0.9497 (mm) cc_final: 0.8912 (mt) REVERT: c 492 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8433 (mp0) REVERT: d 530 MET cc_start: 0.8045 (mmp) cc_final: 0.7803 (mmp) REVERT: d 588 ARG cc_start: 0.8984 (mtt180) cc_final: 0.8753 (ttm-80) REVERT: d 589 ASP cc_start: 0.8871 (m-30) cc_final: 0.8625 (m-30) REVERT: d 591 GLN cc_start: 0.9431 (tm-30) cc_final: 0.9097 (tm-30) REVERT: d 626 MET cc_start: 0.8400 (mtt) cc_final: 0.8131 (mtt) REVERT: d 633 LYS cc_start: 0.9314 (mmmm) cc_final: 0.9099 (mmmm) REVERT: d 655 LYS cc_start: 0.9398 (mmmm) cc_final: 0.9049 (pttp) REVERT: h 51 MET cc_start: 0.3302 (ttp) cc_final: 0.2938 (ttp) REVERT: h 55 GLU cc_start: 0.5171 (mm-30) cc_final: 0.4885 (mm-30) REVERT: l 4 MET cc_start: 0.4191 (mmm) cc_final: 0.3768 (mtp) REVERT: q 28 ASN cc_start: 0.8980 (t0) cc_final: 0.8585 (t0) REVERT: q 52 LYS cc_start: 0.9286 (mtmm) cc_final: 0.8598 (mtmm) REVERT: q 72 GLN cc_start: 0.9313 (tt0) cc_final: 0.8964 (tm-30) REVERT: q 73 LEU cc_start: 0.9008 (mt) cc_final: 0.8532 (mp) REVERT: q 76 ASP cc_start: 0.5960 (p0) cc_final: 0.5562 (p0) REVERT: q 105 GLN cc_start: 0.9153 (pp30) cc_final: 0.8779 (pp30) REVERT: r 32 MET cc_start: 0.8924 (tpt) cc_final: 0.8601 (tpt) REVERT: r 33 THR cc_start: 0.9075 (m) cc_final: 0.8747 (p) REVERT: r 77 LEU cc_start: 0.9387 (mt) cc_final: 0.9066 (tt) outliers start: 4 outliers final: 0 residues processed: 531 average time/residue: 0.2160 time to fit residues: 179.0068 Evaluate side-chains 380 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 226 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 178 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 chunk 336 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 146 optimal weight: 0.0370 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 103 GLN 2 293 GLN ** 2 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 89 GLN 6 42 GLN 7 6 GLN C 80 ASN C 103 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN M 1 GLN ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN R 6 GLN c 80 ASN d 577 GLN l 6 GLN q 6 GLN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 30 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.091019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.064209 restraints weight = 123103.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.066615 restraints weight = 64574.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.068183 restraints weight = 42354.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.069169 restraints weight = 31933.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.069843 restraints weight = 26645.385| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32778 Z= 0.136 Angle : 0.707 13.224 44787 Z= 0.346 Chirality : 0.045 0.224 5322 Planarity : 0.005 0.100 5454 Dihedral : 5.416 43.819 4149 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.12 % Allowed : 2.75 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.13), residues: 3786 helix: 0.82 (0.27), residues: 381 sheet: -0.96 (0.13), residues: 1278 loop : -1.46 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 6 31 TYR 0.017 0.001 TYR D 638 PHE 0.027 0.002 PHE A 519 TRP 0.017 0.001 TRP d 631 HIS 0.004 0.001 HIS c 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (32598) covalent geometry : angle 0.67516 / 0.34 (44292) SS BOND : bond 0.00269 / 0.15 ( 45) SS BOND : angle 2.04311 / 1.38 ( 90) hydrogen bonds : bond 0.03558 / 2.36 ( 1043) hydrogen bonds : angle 5.67257 / 3.89 ( 2832) link_ALPHA1-2 : bond 0.00758 / 0.40 ( 6) link_ALPHA1-2 : angle 1.79043 / 1.03 ( 18) link_ALPHA1-3 : bond 0.00655 / 0.45 ( 18) link_ALPHA1-3 : angle 1.66874 / 1.15 ( 54) link_ALPHA1-6 : bond 0.00376 / 0.24 ( 9) link_ALPHA1-6 : angle 1.58308 / 0.99 ( 27) link_BETA1-4 : bond 0.00414 / 0.26 ( 57) link_BETA1-4 : angle 2.33474 / 1.65 ( 171) link_NAG-ASN : bond 0.00366 / 0.22 ( 45) link_NAG-ASN : angle 2.10753 / 1.48 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 548 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 45 TRP cc_start: 0.9027 (p90) cc_final: 0.8595 (p90) REVERT: 2 47 ASP cc_start: 0.8474 (t0) cc_final: 0.7567 (m-30) REVERT: 2 52 LEU cc_start: 0.9440 (mt) cc_final: 0.9156 (mm) REVERT: 2 83 GLU cc_start: 0.8854 (pt0) cc_final: 0.8258 (pm20) REVERT: 2 104 MET cc_start: 0.9102 (tmm) cc_final: 0.8606 (tmm) REVERT: 2 119 CYS cc_start: 0.6710 (m) cc_final: 0.6363 (m) REVERT: 2 443 ILE cc_start: 0.8637 (mm) cc_final: 0.8400 (tt) REVERT: 2 492 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8534 (mm-30) REVERT: 3 23 GLU cc_start: 0.9215 (tp30) cc_final: 0.8966 (tp30) REVERT: 3 51 MET cc_start: 0.2278 (ttp) cc_final: 0.1575 (ttm) REVERT: 3 53 ASN cc_start: 0.8422 (m-40) cc_final: 0.7961 (p0) REVERT: 3 55 GLU cc_start: 0.5877 (mm-30) cc_final: 0.5279 (mm-30) REVERT: 3 71 LYS cc_start: 0.5117 (ptpt) cc_final: 0.4741 (mtpt) REVERT: 5 100 LYS cc_start: 0.9374 (mmmm) cc_final: 0.8493 (tmtt) REVERT: 5 103 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8433 (mmtm) REVERT: 6 26 GLU cc_start: 0.8778 (tp30) cc_final: 0.8578 (tp30) REVERT: 7 33 THR cc_start: 0.9088 (m) cc_final: 0.8848 (m) REVERT: 7 46 LEU cc_start: 0.9518 (mp) cc_final: 0.9278 (mp) REVERT: 7 77 LEU cc_start: 0.9286 (mt) cc_final: 0.9060 (tp) REVERT: 8 47 TRP cc_start: 0.8806 (t60) cc_final: 0.8312 (t60) REVERT: 8 72 GLN cc_start: 0.9356 (tt0) cc_final: 0.9096 (tp40) REVERT: A 588 ARG cc_start: 0.9082 (mtt180) cc_final: 0.8614 (ttm110) REVERT: A 589 ASP cc_start: 0.8790 (m-30) cc_final: 0.8481 (m-30) REVERT: A 591 GLN cc_start: 0.9421 (tm-30) cc_final: 0.9007 (tm-30) REVERT: A 632 ASP cc_start: 0.8916 (t0) cc_final: 0.8710 (t70) REVERT: C 45 TRP cc_start: 0.8941 (p90) cc_final: 0.8310 (p90) REVERT: C 83 GLU cc_start: 0.8983 (pt0) cc_final: 0.8467 (pm20) REVERT: C 161 MET cc_start: 0.9190 (tpp) cc_final: 0.8537 (tpp) REVERT: C 259 LEU cc_start: 0.8769 (mp) cc_final: 0.8532 (pp) REVERT: C 492 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8394 (mp0) REVERT: D 586 TYR cc_start: 0.9458 (t80) cc_final: 0.9162 (t80) REVERT: H 51 MET cc_start: 0.2953 (ttm) cc_final: 0.2727 (ttm) REVERT: H 53 ASN cc_start: 0.8226 (m-40) cc_final: 0.7967 (p0) REVERT: H 55 GLU cc_start: 0.5684 (mm-30) cc_final: 0.5434 (mm-30) REVERT: L 4 MET cc_start: 0.3606 (mmm) cc_final: 0.2788 (mtp) REVERT: L 92 PHE cc_start: 0.8282 (t80) cc_final: 0.7994 (t80) REVERT: M 105 THR cc_start: 0.7867 (m) cc_final: 0.7576 (p) REVERT: Q 72 GLN cc_start: 0.9235 (tt0) cc_final: 0.9027 (tp40) REVERT: Q 89 GLU cc_start: 0.6764 (tm-30) cc_final: 0.6316 (tm-30) REVERT: Q 105 GLN cc_start: 0.9222 (pp30) cc_final: 0.9021 (pp30) REVERT: R 33 THR cc_start: 0.8998 (m) cc_final: 0.8752 (m) REVERT: R 45 LEU cc_start: 0.9109 (mt) cc_final: 0.8821 (mt) REVERT: R 46 LEU cc_start: 0.9117 (mp) cc_final: 0.8865 (mp) REVERT: R 53 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.7904 (mtm-85) REVERT: c 83 GLU cc_start: 0.8786 (pt0) cc_final: 0.8339 (pm20) REVERT: c 100 MET cc_start: 0.9229 (ptt) cc_final: 0.8978 (ptp) REVERT: c 123 THR cc_start: 0.9261 (p) cc_final: 0.8861 (t) REVERT: c 321 ASP cc_start: 0.8359 (t0) cc_final: 0.7838 (t0) REVERT: c 425 ASN cc_start: 0.8911 (t0) cc_final: 0.8510 (t0) REVERT: c 491 ILE cc_start: 0.9440 (mm) cc_final: 0.9067 (mp) REVERT: c 492 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8340 (mp0) REVERT: d 530 MET cc_start: 0.7800 (mmp) cc_final: 0.7462 (mmp) REVERT: d 588 ARG cc_start: 0.9044 (mtt180) cc_final: 0.8773 (ttm-80) REVERT: d 589 ASP cc_start: 0.8884 (m-30) cc_final: 0.8574 (m-30) REVERT: d 591 GLN cc_start: 0.9421 (tm-30) cc_final: 0.9086 (tm-30) REVERT: d 643 TYR cc_start: 0.9194 (m-10) cc_final: 0.8972 (m-10) REVERT: d 655 LYS cc_start: 0.9459 (mmmm) cc_final: 0.9061 (pttp) REVERT: h 51 MET cc_start: 0.3057 (ttp) cc_final: 0.2807 (ttm) REVERT: h 55 GLU cc_start: 0.5256 (mm-30) cc_final: 0.5020 (mm-30) REVERT: l 4 MET cc_start: 0.3558 (mmm) cc_final: 0.3124 (mtp) REVERT: m 100 LYS cc_start: 0.9386 (mmmm) cc_final: 0.8652 (tmtt) REVERT: q 28 ASN cc_start: 0.8955 (t0) cc_final: 0.8528 (t0) REVERT: q 52 LYS cc_start: 0.9369 (mtmm) cc_final: 0.8660 (mtmm) REVERT: q 73 LEU cc_start: 0.9013 (mt) cc_final: 0.8629 (mt) REVERT: q 76 ASP cc_start: 0.8028 (p0) cc_final: 0.7768 (p0) REVERT: r 11 LEU cc_start: 0.9057 (tt) cc_final: 0.8555 (mt) REVERT: r 33 THR cc_start: 0.9031 (m) cc_final: 0.8695 (p) REVERT: r 77 LEU cc_start: 0.9300 (mt) cc_final: 0.9025 (tt) outliers start: 4 outliers final: 0 residues processed: 552 average time/residue: 0.2090 time to fit residues: 180.2671 Evaluate side-chains 395 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 190 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 217 optimal weight: 10.0000 chunk 233 optimal weight: 0.4980 chunk 141 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 205 optimal weight: 6.9990 chunk 336 optimal weight: 0.4980 chunk 240 optimal weight: 0.9990 chunk 326 optimal weight: 20.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 428 GLN 5 1 GLN 6 42 GLN C 80 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 1 GLN ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 377 ASN ** d 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 68 HIS n 37 GLN ** q 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 30 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.091590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.064714 restraints weight = 122404.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.067113 restraints weight = 64705.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.068707 restraints weight = 42609.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.069708 restraints weight = 32213.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.070233 restraints weight = 26880.565| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32778 Z= 0.125 Angle : 0.693 13.624 44787 Z= 0.338 Chirality : 0.045 0.215 5322 Planarity : 0.005 0.078 5454 Dihedral : 5.249 48.244 4149 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.03 % Allowed : 1.94 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.13), residues: 3786 helix: 0.99 (0.27), residues: 381 sheet: -0.80 (0.14), residues: 1272 loop : -1.34 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 3 81 TYR 0.020 0.001 TYR n 87 PHE 0.028 0.001 PHE d 519 TRP 0.025 0.001 TRP C 427 HIS 0.008 0.001 HIS c 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (32598) covalent geometry : angle 0.66225 / 0.33 (44292) SS BOND : bond 0.00193 / 0.12 ( 45) SS BOND : angle 2.03962 / 1.38 ( 90) hydrogen bonds : bond 0.03359 / 2.21 ( 1043) hydrogen bonds : angle 5.44848 / 3.74 ( 2832) link_ALPHA1-2 : bond 0.00603 / 0.31 ( 6) link_ALPHA1-2 : angle 1.67022 / 0.97 ( 18) link_ALPHA1-3 : bond 0.00680 / 0.46 ( 18) link_ALPHA1-3 : angle 1.62810 / 1.10 ( 54) link_ALPHA1-6 : bond 0.00377 / 0.24 ( 9) link_ALPHA1-6 : angle 1.55149 / 0.99 ( 27) link_BETA1-4 : bond 0.00413 / 0.26 ( 57) link_BETA1-4 : angle 2.28179 / 1.60 ( 171) link_NAG-ASN : bond 0.00352 / 0.23 ( 45) link_NAG-ASN : angle 2.00625 / 1.41 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 528 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 45 TRP cc_start: 0.9025 (p90) cc_final: 0.8611 (p90) REVERT: 2 47 ASP cc_start: 0.8424 (t0) cc_final: 0.7825 (m-30) REVERT: 2 83 GLU cc_start: 0.8888 (pt0) cc_final: 0.8247 (pm20) REVERT: 2 119 CYS cc_start: 0.6494 (m) cc_final: 0.6084 (m) REVERT: 2 492 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8538 (mm-30) REVERT: 3 23 GLU cc_start: 0.9219 (tp30) cc_final: 0.9003 (tp30) REVERT: 3 51 MET cc_start: 0.2078 (ttp) cc_final: 0.1455 (ttm) REVERT: 3 53 ASN cc_start: 0.8368 (m-40) cc_final: 0.8153 (p0) REVERT: 3 55 GLU cc_start: 0.5920 (mm-30) cc_final: 0.5383 (mm-30) REVERT: 3 71 LYS cc_start: 0.5093 (ptpt) cc_final: 0.4862 (mtpt) REVERT: 5 100 LYS cc_start: 0.9445 (mmmm) cc_final: 0.8546 (tmtt) REVERT: 6 26 GLU cc_start: 0.8837 (tp30) cc_final: 0.8624 (tp30) REVERT: 7 11 LEU cc_start: 0.9011 (tt) cc_final: 0.8653 (mt) REVERT: 7 33 THR cc_start: 0.9022 (m) cc_final: 0.8785 (m) REVERT: 7 77 LEU cc_start: 0.9239 (mt) cc_final: 0.9037 (tp) REVERT: 8 27 TYR cc_start: 0.8726 (p90) cc_final: 0.8129 (p90) REVERT: 8 47 TRP cc_start: 0.8896 (t60) cc_final: 0.8252 (t60) REVERT: A 530 MET cc_start: 0.8331 (mmm) cc_final: 0.7863 (mmt) REVERT: A 588 ARG cc_start: 0.9057 (mtt180) cc_final: 0.8560 (ttm110) REVERT: A 589 ASP cc_start: 0.8762 (m-30) cc_final: 0.8470 (m-30) REVERT: A 591 GLN cc_start: 0.9417 (tm-30) cc_final: 0.8952 (tm-30) REVERT: A 632 ASP cc_start: 0.8866 (t0) cc_final: 0.8657 (t70) REVERT: A 655 LYS cc_start: 0.9003 (pttp) cc_final: 0.8696 (pttm) REVERT: C 45 TRP cc_start: 0.8923 (p90) cc_final: 0.8353 (p90) REVERT: C 104 MET cc_start: 0.9135 (tmm) cc_final: 0.8833 (tmm) REVERT: C 161 MET cc_start: 0.9199 (tpp) cc_final: 0.8511 (tpp) REVERT: C 492 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8339 (mp0) REVERT: D 586 TYR cc_start: 0.9454 (t80) cc_final: 0.9220 (t80) REVERT: D 655 LYS cc_start: 0.8972 (pttp) cc_final: 0.8659 (mmmt) REVERT: H 51 MET cc_start: 0.2575 (ttm) cc_final: 0.1888 (ttm) REVERT: H 53 ASN cc_start: 0.8398 (m-40) cc_final: 0.8178 (p0) REVERT: H 55 GLU cc_start: 0.5727 (mm-30) cc_final: 0.5329 (mm-30) REVERT: L 4 MET cc_start: 0.4087 (mmm) cc_final: 0.3602 (mtp) REVERT: L 92 PHE cc_start: 0.8321 (t80) cc_final: 0.7996 (t80) REVERT: M 80 LEU cc_start: 0.8513 (tt) cc_final: 0.7996 (tt) REVERT: M 103 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8009 (mmtm) REVERT: M 105 THR cc_start: 0.7843 (m) cc_final: 0.7551 (p) REVERT: Q 69 MET cc_start: 0.9336 (mtt) cc_final: 0.9111 (mtp) REVERT: Q 89 GLU cc_start: 0.6678 (tm-30) cc_final: 0.6344 (tm-30) REVERT: R 33 THR cc_start: 0.9070 (m) cc_final: 0.8751 (m) REVERT: R 45 LEU cc_start: 0.9094 (mt) cc_final: 0.8656 (mp) REVERT: R 53 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.7619 (mtm-85) REVERT: c 83 GLU cc_start: 0.8847 (pt0) cc_final: 0.8346 (pm20) REVERT: c 100 MET cc_start: 0.9282 (ptt) cc_final: 0.9035 (ptp) REVERT: c 104 MET cc_start: 0.9106 (tmm) cc_final: 0.8590 (tmm) REVERT: c 123 THR cc_start: 0.9211 (p) cc_final: 0.8786 (t) REVERT: c 425 ASN cc_start: 0.8909 (t0) cc_final: 0.8495 (t0) REVERT: c 492 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8365 (mp0) REVERT: d 530 MET cc_start: 0.7715 (mmp) cc_final: 0.7340 (mmp) REVERT: d 586 TYR cc_start: 0.9515 (t80) cc_final: 0.9273 (t80) REVERT: d 588 ARG cc_start: 0.9000 (mtt180) cc_final: 0.8700 (ttm-80) REVERT: d 589 ASP cc_start: 0.8841 (m-30) cc_final: 0.8545 (m-30) REVERT: d 655 LYS cc_start: 0.9436 (mmmm) cc_final: 0.8982 (pttp) REVERT: h 51 MET cc_start: 0.2924 (ttp) cc_final: 0.2571 (ttm) REVERT: h 55 GLU cc_start: 0.5299 (mm-30) cc_final: 0.5068 (mm-30) REVERT: l 4 MET cc_start: 0.4225 (mmm) cc_final: 0.4001 (mtp) REVERT: m 100 LYS cc_start: 0.9434 (mmmm) cc_final: 0.8565 (tmtt) REVERT: q 28 ASN cc_start: 0.8873 (t0) cc_final: 0.8399 (t0) REVERT: q 52 LYS cc_start: 0.9402 (mtmm) cc_final: 0.8622 (mtmm) REVERT: q 73 LEU cc_start: 0.9117 (mt) cc_final: 0.8845 (mt) REVERT: r 11 LEU cc_start: 0.9027 (tt) cc_final: 0.8491 (mt) REVERT: r 21 LEU cc_start: 0.8655 (mt) cc_final: 0.8454 (mm) REVERT: r 32 MET cc_start: 0.8986 (tpt) cc_final: 0.8762 (tpt) REVERT: r 33 THR cc_start: 0.9014 (m) cc_final: 0.8704 (p) REVERT: r 77 LEU cc_start: 0.9202 (mt) cc_final: 0.8806 (tt) outliers start: 1 outliers final: 0 residues processed: 529 average time/residue: 0.2009 time to fit residues: 167.5940 Evaluate side-chains 390 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 206 optimal weight: 0.0050 chunk 371 optimal weight: 0.1980 chunk 151 optimal weight: 8.9990 chunk 323 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 246 optimal weight: 9.9990 chunk 101 optimal weight: 0.4980 chunk 201 optimal weight: 20.0000 chunk 324 optimal weight: 5.9990 chunk 291 optimal weight: 2.9990 chunk 199 optimal weight: 0.0670 overall best weight: 0.7534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 1 GLN 6 42 GLN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 1 GLN ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 591 GLN l 55 GLN ** q 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 30 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.091846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.065112 restraints weight = 121818.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.067501 restraints weight = 63924.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.069081 restraints weight = 41892.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.070082 restraints weight = 31611.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.070731 restraints weight = 26240.729| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32778 Z= 0.121 Angle : 0.677 13.773 44787 Z= 0.330 Chirality : 0.044 0.212 5322 Planarity : 0.004 0.072 5454 Dihedral : 5.164 50.600 4149 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.13), residues: 3786 helix: 1.16 (0.28), residues: 381 sheet: -0.65 (0.14), residues: 1290 loop : -1.30 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 3 81 TYR 0.019 0.001 TYR C 486 PHE 0.022 0.001 PHE A 519 TRP 0.031 0.001 TRP 2 427 HIS 0.004 0.001 HIS c 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (32598) covalent geometry : angle 0.64814 / 0.32 (44292) SS BOND : bond 0.00170 / 0.11 ( 45) SS BOND : angle 1.89412 / 1.29 ( 90) hydrogen bonds : bond 0.03298 / 2.17 ( 1043) hydrogen bonds : angle 5.29585 / 3.63 ( 2832) link_ALPHA1-2 : bond 0.00556 / 0.29 ( 6) link_ALPHA1-2 : angle 1.61607 / 0.94 ( 18) link_ALPHA1-3 : bond 0.00658 / 0.44 ( 18) link_ALPHA1-3 : angle 1.61146 / 1.09 ( 54) link_ALPHA1-6 : bond 0.00370 / 0.23 ( 9) link_ALPHA1-6 : angle 1.54270 / 0.98 ( 27) link_BETA1-4 : bond 0.00410 / 0.25 ( 57) link_BETA1-4 : angle 2.23884 / 1.57 ( 171) link_NAG-ASN : bond 0.00330 / 0.21 ( 45) link_NAG-ASN : angle 1.95529 / 1.37 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 517 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 45 TRP cc_start: 0.9047 (p90) cc_final: 0.8632 (p90) REVERT: 2 52 LEU cc_start: 0.9404 (mt) cc_final: 0.9159 (mm) REVERT: 2 83 GLU cc_start: 0.8867 (pt0) cc_final: 0.8233 (pm20) REVERT: 2 119 CYS cc_start: 0.6695 (m) cc_final: 0.6366 (m) REVERT: 2 425 ASN cc_start: 0.8693 (t0) cc_final: 0.8172 (t0) REVERT: 2 492 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8476 (mm-30) REVERT: 3 23 GLU cc_start: 0.9203 (tp30) cc_final: 0.8973 (tp30) REVERT: 3 51 MET cc_start: 0.2135 (ttp) cc_final: 0.1188 (ttm) REVERT: 3 53 ASN cc_start: 0.8371 (m-40) cc_final: 0.8105 (p0) REVERT: 3 55 GLU cc_start: 0.5870 (mm-30) cc_final: 0.5387 (mm-30) REVERT: 3 71 LYS cc_start: 0.5355 (ptpt) cc_final: 0.5092 (ptpt) REVERT: 5 100 LYS cc_start: 0.9446 (mmmm) cc_final: 0.8556 (tmtt) REVERT: 7 33 THR cc_start: 0.8918 (m) cc_final: 0.8717 (m) REVERT: 7 46 LEU cc_start: 0.9538 (mp) cc_final: 0.9330 (mp) REVERT: 7 77 LEU cc_start: 0.9260 (mt) cc_final: 0.9033 (tp) REVERT: 8 27 TYR cc_start: 0.8689 (p90) cc_final: 0.8397 (p90) REVERT: 8 47 TRP cc_start: 0.8923 (t60) cc_final: 0.8288 (t60) REVERT: A 588 ARG cc_start: 0.9091 (mtt180) cc_final: 0.8607 (ttm110) REVERT: A 589 ASP cc_start: 0.8786 (m-30) cc_final: 0.8468 (m-30) REVERT: A 591 GLN cc_start: 0.9439 (tm-30) cc_final: 0.8711 (tm-30) REVERT: A 595 ILE cc_start: 0.9646 (pt) cc_final: 0.9418 (mt) REVERT: A 655 LYS cc_start: 0.8987 (pttp) cc_final: 0.8723 (pttp) REVERT: C 45 TRP cc_start: 0.8930 (p90) cc_final: 0.8224 (p90) REVERT: C 161 MET cc_start: 0.9228 (tpp) cc_final: 0.8554 (tpp) REVERT: C 492 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8300 (mp0) REVERT: D 574 LYS cc_start: 0.9330 (ptpt) cc_final: 0.8980 (pttt) REVERT: D 580 VAL cc_start: 0.9566 (m) cc_final: 0.9325 (m) REVERT: D 586 TYR cc_start: 0.9444 (t80) cc_final: 0.9097 (t80) REVERT: D 655 LYS cc_start: 0.9007 (pttp) cc_final: 0.8513 (mmmm) REVERT: H 51 MET cc_start: 0.2661 (ttm) cc_final: 0.1952 (ttm) REVERT: H 53 ASN cc_start: 0.8370 (m-40) cc_final: 0.8168 (p0) REVERT: H 55 GLU cc_start: 0.5728 (mm-30) cc_final: 0.5297 (mm-30) REVERT: L 4 MET cc_start: 0.3629 (mmm) cc_final: 0.3139 (mtp) REVERT: L 92 PHE cc_start: 0.8227 (t80) cc_final: 0.7919 (t80) REVERT: M 80 LEU cc_start: 0.8589 (tt) cc_final: 0.8088 (tt) REVERT: M 100 LYS cc_start: 0.9440 (mmmm) cc_final: 0.8885 (tppt) REVERT: M 105 THR cc_start: 0.7892 (m) cc_final: 0.7598 (p) REVERT: Q 28 ASN cc_start: 0.8722 (t0) cc_final: 0.8365 (t0) REVERT: Q 89 GLU cc_start: 0.6871 (tm-30) cc_final: 0.6560 (tm-30) REVERT: R 33 THR cc_start: 0.9058 (m) cc_final: 0.8754 (m) REVERT: R 45 LEU cc_start: 0.9103 (mt) cc_final: 0.8686 (mp) REVERT: R 53 ARG cc_start: 0.8622 (mtm-85) cc_final: 0.7989 (mtm-85) REVERT: c 83 GLU cc_start: 0.8832 (pt0) cc_final: 0.8317 (pm20) REVERT: c 100 MET cc_start: 0.9342 (ptt) cc_final: 0.9063 (ptp) REVERT: c 104 MET cc_start: 0.9237 (tmm) cc_final: 0.8662 (tmm) REVERT: c 123 THR cc_start: 0.9183 (p) cc_final: 0.8739 (t) REVERT: c 321 ASP cc_start: 0.8243 (t0) cc_final: 0.8017 (t0) REVERT: c 425 ASN cc_start: 0.8897 (t0) cc_final: 0.8494 (t0) REVERT: c 492 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8403 (mm-30) REVERT: d 530 MET cc_start: 0.7730 (mmp) cc_final: 0.7275 (mmp) REVERT: d 574 LYS cc_start: 0.9075 (pttp) cc_final: 0.8740 (pttm) REVERT: d 586 TYR cc_start: 0.9491 (t80) cc_final: 0.9252 (t80) REVERT: d 588 ARG cc_start: 0.9001 (mtt180) cc_final: 0.8718 (ttm-80) REVERT: d 589 ASP cc_start: 0.8860 (m-30) cc_final: 0.8558 (m-30) REVERT: d 633 LYS cc_start: 0.9116 (mmmm) cc_final: 0.8733 (mmtm) REVERT: d 655 LYS cc_start: 0.9411 (mmmm) cc_final: 0.8974 (pttp) REVERT: h 51 MET cc_start: 0.2894 (ttp) cc_final: 0.2485 (ttm) REVERT: h 55 GLU cc_start: 0.5393 (mm-30) cc_final: 0.5141 (mm-30) REVERT: l 4 MET cc_start: 0.3717 (mmm) cc_final: 0.3317 (mtp) REVERT: m 100 LYS cc_start: 0.9477 (mmmm) cc_final: 0.8598 (tmtt) REVERT: q 28 ASN cc_start: 0.8860 (t0) cc_final: 0.8510 (t0) REVERT: q 52 LYS cc_start: 0.9395 (mtmm) cc_final: 0.8592 (mtmm) REVERT: q 73 LEU cc_start: 0.9082 (mt) cc_final: 0.8816 (mt) REVERT: r 11 LEU cc_start: 0.9024 (tt) cc_final: 0.8493 (mt) REVERT: r 33 THR cc_start: 0.8853 (m) cc_final: 0.8545 (p) REVERT: r 77 LEU cc_start: 0.9183 (mt) cc_final: 0.8949 (tp) outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.2039 time to fit residues: 165.7491 Evaluate side-chains 393 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 249 optimal weight: 0.2980 chunk 188 optimal weight: 7.9990 chunk 322 optimal weight: 30.0000 chunk 151 optimal weight: 3.9990 chunk 343 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 236 optimal weight: 2.9990 chunk 224 optimal weight: 10.0000 chunk 312 optimal weight: 0.4980 chunk 369 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 80 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 42 GLN A 577 GLN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN Q 105 GLN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.090073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.063177 restraints weight = 125377.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.065460 restraints weight = 66873.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.066973 restraints weight = 44480.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.067955 restraints weight = 33895.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.068574 restraints weight = 28400.583| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32778 Z= 0.168 Angle : 0.699 13.663 44787 Z= 0.339 Chirality : 0.045 0.231 5322 Planarity : 0.005 0.075 5454 Dihedral : 5.128 47.548 4149 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.03 % Allowed : 1.65 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.14), residues: 3786 helix: 0.92 (0.28), residues: 399 sheet: -0.63 (0.14), residues: 1266 loop : -1.24 (0.14), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 3 81 TYR 0.022 0.001 TYR q 32 PHE 0.018 0.002 PHE d 519 TRP 0.030 0.002 TRP d 571 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (32598) covalent geometry : angle 0.66901 / 0.33 (44292) SS BOND : bond 0.00246 / 0.16 ( 45) SS BOND : angle 1.70124 / 1.15 ( 90) hydrogen bonds : bond 0.03475 / 2.30 ( 1043) hydrogen bonds : angle 5.37461 / 3.68 ( 2832) link_ALPHA1-2 : bond 0.00625 / 0.34 ( 6) link_ALPHA1-2 : angle 1.74997 / 1.00 ( 18) link_ALPHA1-3 : bond 0.00591 / 0.39 ( 18) link_ALPHA1-3 : angle 1.75861 / 1.17 ( 54) link_ALPHA1-6 : bond 0.00364 / 0.23 ( 9) link_ALPHA1-6 : angle 1.49992 / 0.96 ( 27) link_BETA1-4 : bond 0.00351 / 0.22 ( 57) link_BETA1-4 : angle 2.27448 / 1.59 ( 171) link_NAG-ASN : bond 0.00486 / 0.29 ( 45) link_NAG-ASN : angle 2.11586 / 1.47 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 487 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 45 TRP cc_start: 0.9069 (p90) cc_final: 0.8697 (p90) REVERT: 2 52 LEU cc_start: 0.9437 (mt) cc_final: 0.9204 (mm) REVERT: 2 83 GLU cc_start: 0.8867 (pt0) cc_final: 0.8324 (pm20) REVERT: 2 119 CYS cc_start: 0.6503 (m) cc_final: 0.6106 (m) REVERT: 2 207 LYS cc_start: 0.9351 (tppt) cc_final: 0.9120 (ttpp) REVERT: 2 425 ASN cc_start: 0.8622 (t0) cc_final: 0.8110 (t0) REVERT: 2 492 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8506 (mm-30) REVERT: 3 23 GLU cc_start: 0.9171 (tp30) cc_final: 0.8951 (tp30) REVERT: 3 51 MET cc_start: 0.2022 (ttp) cc_final: 0.1043 (ttm) REVERT: 3 53 ASN cc_start: 0.8356 (m-40) cc_final: 0.8091 (p0) REVERT: 3 55 GLU cc_start: 0.5878 (mm-30) cc_final: 0.5449 (mm-30) REVERT: 3 71 LYS cc_start: 0.5496 (ptpt) cc_final: 0.5207 (ptpt) REVERT: 5 100 LYS cc_start: 0.9473 (mmmm) cc_final: 0.8586 (tmtt) REVERT: 7 48 TYR cc_start: 0.8807 (p90) cc_final: 0.8593 (p90) REVERT: A 530 MET cc_start: 0.7710 (mmp) cc_final: 0.7288 (mmp) REVERT: A 588 ARG cc_start: 0.9053 (mtt180) cc_final: 0.8574 (ttm110) REVERT: A 589 ASP cc_start: 0.8768 (m-30) cc_final: 0.8490 (m-30) REVERT: A 591 GLN cc_start: 0.9492 (tm-30) cc_final: 0.8997 (tm-30) REVERT: A 632 ASP cc_start: 0.8893 (t70) cc_final: 0.8535 (t70) REVERT: C 45 TRP cc_start: 0.8965 (p90) cc_final: 0.8252 (p90) REVERT: C 140 ASP cc_start: 0.8049 (m-30) cc_final: 0.7510 (t0) REVERT: C 161 MET cc_start: 0.9296 (tpp) cc_final: 0.8641 (tpp) REVERT: C 492 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8378 (mp0) REVERT: D 574 LYS cc_start: 0.9361 (ptpt) cc_final: 0.9051 (pttt) REVERT: H 51 MET cc_start: 0.2695 (ttm) cc_final: 0.2070 (ttm) REVERT: H 53 ASN cc_start: 0.8373 (m-40) cc_final: 0.8168 (p0) REVERT: H 55 GLU cc_start: 0.5629 (mm-30) cc_final: 0.5159 (mm-30) REVERT: L 4 MET cc_start: 0.3900 (mmm) cc_final: 0.3418 (mtp) REVERT: L 92 PHE cc_start: 0.8312 (t80) cc_final: 0.8021 (t80) REVERT: M 100 LYS cc_start: 0.9512 (mmmm) cc_final: 0.8469 (tmtt) REVERT: M 103 LYS cc_start: 0.8696 (mmmt) cc_final: 0.8169 (mmtm) REVERT: M 105 THR cc_start: 0.7996 (m) cc_final: 0.7710 (p) REVERT: Q 76 ASP cc_start: 0.8279 (m-30) cc_final: 0.8076 (m-30) REVERT: Q 89 GLU cc_start: 0.6861 (tm-30) cc_final: 0.6603 (tm-30) REVERT: R 32 MET cc_start: 0.8880 (tpt) cc_final: 0.8672 (tpt) REVERT: R 33 THR cc_start: 0.8932 (m) cc_final: 0.8716 (m) REVERT: R 45 LEU cc_start: 0.9149 (mt) cc_final: 0.8850 (mp) REVERT: R 59 ASP cc_start: 0.9416 (t0) cc_final: 0.9184 (t0) REVERT: c 83 GLU cc_start: 0.8822 (pt0) cc_final: 0.8334 (pm20) REVERT: c 100 MET cc_start: 0.9310 (ptt) cc_final: 0.9014 (ptp) REVERT: c 123 THR cc_start: 0.9201 (p) cc_final: 0.8762 (t) REVERT: c 321 ASP cc_start: 0.8252 (t0) cc_final: 0.8002 (t0) REVERT: c 425 ASN cc_start: 0.8995 (t0) cc_final: 0.8397 (t0) REVERT: c 492 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8406 (mp0) REVERT: d 530 MET cc_start: 0.7768 (mmp) cc_final: 0.7307 (mmp) REVERT: d 574 LYS cc_start: 0.9228 (pttp) cc_final: 0.9025 (pttm) REVERT: d 586 TYR cc_start: 0.9550 (t80) cc_final: 0.9320 (t80) REVERT: d 588 ARG cc_start: 0.9028 (mtt180) cc_final: 0.8649 (ttm-80) REVERT: d 589 ASP cc_start: 0.8860 (m-30) cc_final: 0.8586 (m-30) REVERT: d 595 ILE cc_start: 0.9619 (pt) cc_final: 0.9410 (pt) REVERT: d 633 LYS cc_start: 0.9134 (mmmm) cc_final: 0.8742 (mmtm) REVERT: d 655 LYS cc_start: 0.9413 (mmmm) cc_final: 0.8961 (pttp) REVERT: h 51 MET cc_start: 0.2857 (ttp) cc_final: 0.2451 (ttm) REVERT: h 55 GLU cc_start: 0.5189 (mm-30) cc_final: 0.4950 (mm-30) REVERT: l 4 MET cc_start: 0.3812 (mmm) cc_final: 0.3396 (mtp) REVERT: m 100 LYS cc_start: 0.9474 (mmmm) cc_final: 0.8617 (tmtt) REVERT: q 28 ASN cc_start: 0.8774 (t0) cc_final: 0.7975 (t0) REVERT: q 52 LYS cc_start: 0.9386 (mtmm) cc_final: 0.8730 (mtmm) REVERT: r 11 LEU cc_start: 0.9074 (tt) cc_final: 0.8557 (mt) REVERT: r 77 LEU cc_start: 0.9221 (mt) cc_final: 0.9003 (tp) outliers start: 1 outliers final: 0 residues processed: 488 average time/residue: 0.2021 time to fit residues: 154.2928 Evaluate side-chains 365 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 280 optimal weight: 0.2980 chunk 149 optimal weight: 2.9990 chunk 284 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 91 optimal weight: 30.0000 chunk 179 optimal weight: 0.9980 chunk 204 optimal weight: 0.0970 chunk 197 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 42 GLN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 GLN ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN Q 105 GLN d 543 ASN d 577 GLN d 591 GLN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 55 GLN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.090166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.063343 restraints weight = 124297.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.065657 restraints weight = 66059.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.067181 restraints weight = 43708.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.068143 restraints weight = 33205.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 72)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.068771 restraints weight = 27714.218| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32778 Z= 0.152 Angle : 0.702 13.853 44787 Z= 0.342 Chirality : 0.045 0.233 5322 Planarity : 0.005 0.140 5454 Dihedral : 5.117 48.044 4149 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.03 % Allowed : 1.08 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.13), residues: 3786 helix: 0.82 (0.27), residues: 417 sheet: -0.62 (0.14), residues: 1281 loop : -1.26 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG 6 39 TYR 0.040 0.002 TYR D 643 PHE 0.019 0.001 PHE Q 91 TRP 0.021 0.001 TRP d 631 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (32598) covalent geometry : angle 0.67442 / 0.34 (44292) SS BOND : bond 0.00215 / 0.13 ( 45) SS BOND : angle 1.77041 / 1.20 ( 90) hydrogen bonds : bond 0.03427 / 2.27 ( 1043) hydrogen bonds : angle 5.33450 / 3.65 ( 2832) link_ALPHA1-2 : bond 0.00613 / 0.32 ( 6) link_ALPHA1-2 : angle 1.67469 / 0.97 ( 18) link_ALPHA1-3 : bond 0.00675 / 0.46 ( 18) link_ALPHA1-3 : angle 1.71012 / 1.15 ( 54) link_ALPHA1-6 : bond 0.00372 / 0.24 ( 9) link_ALPHA1-6 : angle 1.52672 / 0.96 ( 27) link_BETA1-4 : bond 0.00371 / 0.23 ( 57) link_BETA1-4 : angle 2.22582 / 1.56 ( 171) link_NAG-ASN : bond 0.00386 / 0.23 ( 45) link_NAG-ASN : angle 2.01575 / 1.42 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 478 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 45 TRP cc_start: 0.9066 (p90) cc_final: 0.8701 (p90) REVERT: 2 52 LEU cc_start: 0.9441 (mt) cc_final: 0.9192 (mm) REVERT: 2 83 GLU cc_start: 0.8834 (pt0) cc_final: 0.8297 (pm20) REVERT: 2 119 CYS cc_start: 0.6511 (m) cc_final: 0.6130 (m) REVERT: 2 425 ASN cc_start: 0.8612 (t0) cc_final: 0.8115 (t0) REVERT: 2 492 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8404 (mm-30) REVERT: 3 23 GLU cc_start: 0.9161 (tp30) cc_final: 0.8957 (tp30) REVERT: 3 51 MET cc_start: 0.2075 (ttp) cc_final: 0.0976 (ttm) REVERT: 3 53 ASN cc_start: 0.8303 (m-40) cc_final: 0.8064 (p0) REVERT: 3 55 GLU cc_start: 0.5798 (mm-30) cc_final: 0.5393 (mm-30) REVERT: 3 81 ARG cc_start: 0.8578 (ttp-110) cc_final: 0.7962 (ptp90) REVERT: 5 103 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8423 (mmtm) REVERT: 7 48 TYR cc_start: 0.8751 (p90) cc_final: 0.8550 (p90) REVERT: A 530 MET cc_start: 0.7539 (mmp) cc_final: 0.7123 (mmp) REVERT: A 588 ARG cc_start: 0.9038 (mtt180) cc_final: 0.8576 (ttm110) REVERT: A 589 ASP cc_start: 0.8784 (m-30) cc_final: 0.8467 (m-30) REVERT: A 591 GLN cc_start: 0.9487 (tm-30) cc_final: 0.8955 (tm-30) REVERT: A 632 ASP cc_start: 0.8936 (t70) cc_final: 0.8665 (t70) REVERT: A 655 LYS cc_start: 0.8939 (pttp) cc_final: 0.8638 (pttm) REVERT: C 45 TRP cc_start: 0.8941 (p90) cc_final: 0.8346 (p90) REVERT: C 140 ASP cc_start: 0.7950 (m-30) cc_final: 0.7429 (t0) REVERT: C 161 MET cc_start: 0.9273 (tpp) cc_final: 0.8546 (tpp) REVERT: C 425 ASN cc_start: 0.9007 (t0) cc_final: 0.8711 (t0) REVERT: C 492 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8288 (mp0) REVERT: D 574 LYS cc_start: 0.9357 (ptpt) cc_final: 0.9045 (pttt) REVERT: D 580 VAL cc_start: 0.9583 (m) cc_final: 0.9287 (m) REVERT: D 601 LYS cc_start: 0.8170 (mppt) cc_final: 0.7882 (mtmm) REVERT: D 655 LYS cc_start: 0.8922 (pttp) cc_final: 0.8590 (mmmt) REVERT: H 51 MET cc_start: 0.2731 (ttm) cc_final: 0.1739 (ttm) REVERT: H 53 ASN cc_start: 0.8354 (m-40) cc_final: 0.8119 (p0) REVERT: H 55 GLU cc_start: 0.5653 (mm-30) cc_final: 0.5091 (mm-30) REVERT: L 4 MET cc_start: 0.3824 (mmm) cc_final: 0.3293 (mtp) REVERT: L 92 PHE cc_start: 0.8333 (t80) cc_final: 0.8009 (t80) REVERT: M 100 LYS cc_start: 0.9492 (mmmm) cc_final: 0.8564 (tmtt) REVERT: M 103 LYS cc_start: 0.8827 (mmmt) cc_final: 0.8258 (mmtm) REVERT: M 105 THR cc_start: 0.7996 (m) cc_final: 0.7699 (p) REVERT: Q 72 GLN cc_start: 0.8883 (tp-100) cc_final: 0.8679 (tp-100) REVERT: Q 89 GLU cc_start: 0.6849 (tm-30) cc_final: 0.6591 (tm-30) REVERT: Q 105 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.9049 (pp30) REVERT: R 32 MET cc_start: 0.8847 (tpt) cc_final: 0.8633 (tpt) REVERT: R 33 THR cc_start: 0.8865 (m) cc_final: 0.8614 (m) REVERT: R 45 LEU cc_start: 0.9109 (mt) cc_final: 0.8755 (mp) REVERT: R 46 LEU cc_start: 0.9145 (mp) cc_final: 0.8857 (mp) REVERT: R 98 GLU cc_start: 0.8366 (tp30) cc_final: 0.8161 (tp30) REVERT: c 83 GLU cc_start: 0.8782 (pt0) cc_final: 0.8300 (pm20) REVERT: c 100 MET cc_start: 0.9355 (ptt) cc_final: 0.9023 (ptp) REVERT: c 104 MET cc_start: 0.8746 (tmm) cc_final: 0.8248 (tmm) REVERT: c 123 THR cc_start: 0.9188 (p) cc_final: 0.8729 (t) REVERT: c 321 ASP cc_start: 0.8259 (t0) cc_final: 0.8008 (t0) REVERT: c 425 ASN cc_start: 0.8980 (t0) cc_final: 0.8418 (t0) REVERT: c 492 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8392 (mp0) REVERT: d 530 MET cc_start: 0.7706 (mmp) cc_final: 0.7195 (mmp) REVERT: d 588 ARG cc_start: 0.8955 (mtt180) cc_final: 0.8649 (ttm-80) REVERT: d 589 ASP cc_start: 0.8859 (m-30) cc_final: 0.8577 (m-30) REVERT: d 633 LYS cc_start: 0.9165 (mmmm) cc_final: 0.8763 (mmtm) REVERT: d 655 LYS cc_start: 0.9394 (mmmm) cc_final: 0.8965 (pttp) REVERT: h 51 MET cc_start: 0.2997 (ttp) cc_final: 0.2587 (ttm) REVERT: h 55 GLU cc_start: 0.5345 (mm-30) cc_final: 0.5077 (mm-30) REVERT: l 4 MET cc_start: 0.3671 (mmm) cc_final: 0.3246 (mtp) REVERT: m 100 LYS cc_start: 0.9474 (mmmm) cc_final: 0.8618 (tmtt) REVERT: q 28 ASN cc_start: 0.8899 (t0) cc_final: 0.8179 (t0) REVERT: q 31 ASP cc_start: 0.8694 (m-30) cc_final: 0.7985 (m-30) REVERT: q 52 LYS cc_start: 0.9412 (mtmm) cc_final: 0.8713 (mtmm) REVERT: r 32 MET cc_start: 0.8813 (tpt) cc_final: 0.8470 (tpt) outliers start: 1 outliers final: 0 residues processed: 479 average time/residue: 0.2010 time to fit residues: 151.9991 Evaluate side-chains 361 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 361 optimal weight: 0.9980 chunk 307 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 363 optimal weight: 4.9990 chunk 293 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 119 optimal weight: 0.7980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 80 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 42 GLN A 575 GLN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN Q 105 GLN ** c 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 37 GLN ** q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.088726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.061972 restraints weight = 125456.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.064224 restraints weight = 66508.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.065684 restraints weight = 44167.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066638 restraints weight = 33721.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.067216 restraints weight = 28302.263| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32778 Z= 0.189 Angle : 0.737 13.797 44787 Z= 0.357 Chirality : 0.045 0.239 5322 Planarity : 0.005 0.099 5454 Dihedral : 5.183 43.150 4149 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.03 % Allowed : 0.54 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.14), residues: 3786 helix: 0.71 (0.27), residues: 420 sheet: -0.67 (0.14), residues: 1287 loop : -1.27 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 61 TYR 0.020 0.002 TYR C 486 PHE 0.020 0.002 PHE Q 100D TRP 0.024 0.002 TRP d 631 HIS 0.004 0.001 HIS 2 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (32598) covalent geometry : angle 0.70810 / 0.35 (44292) SS BOND : bond 0.00391 / 0.24 ( 45) SS BOND : angle 1.64282 / 1.10 ( 90) hydrogen bonds : bond 0.03527 / 2.34 ( 1043) hydrogen bonds : angle 5.46025 / 3.74 ( 2832) link_ALPHA1-2 : bond 0.00687 / 0.38 ( 6) link_ALPHA1-2 : angle 1.82009 / 1.04 ( 18) link_ALPHA1-3 : bond 0.00588 / 0.40 ( 18) link_ALPHA1-3 : angle 1.82665 / 1.21 ( 54) link_ALPHA1-6 : bond 0.00370 / 0.24 ( 9) link_ALPHA1-6 : angle 1.50405 / 0.96 ( 27) link_BETA1-4 : bond 0.00361 / 0.23 ( 57) link_BETA1-4 : angle 2.29468 / 1.61 ( 171) link_NAG-ASN : bond 0.00531 / 0.32 ( 45) link_NAG-ASN : angle 2.18920 / 1.52 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 449 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 45 TRP cc_start: 0.9120 (p90) cc_final: 0.8752 (p90) REVERT: 2 52 LEU cc_start: 0.9454 (mt) cc_final: 0.9188 (mm) REVERT: 2 83 GLU cc_start: 0.8883 (pt0) cc_final: 0.8272 (pm20) REVERT: 2 119 CYS cc_start: 0.6475 (m) cc_final: 0.6057 (m) REVERT: 2 140 ASP cc_start: 0.7618 (m-30) cc_final: 0.7076 (t0) REVERT: 2 426 MET cc_start: 0.8730 (ptm) cc_final: 0.8438 (ptm) REVERT: 2 492 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8551 (mm-30) REVERT: 3 23 GLU cc_start: 0.9163 (tp30) cc_final: 0.8959 (tp30) REVERT: 3 51 MET cc_start: 0.1511 (ttp) cc_final: 0.0991 (ttm) REVERT: 3 55 GLU cc_start: 0.5665 (mm-30) cc_final: 0.5430 (mm-30) REVERT: 3 71 LYS cc_start: 0.6130 (ptpp) cc_final: 0.5877 (mtmt) REVERT: 3 81 ARG cc_start: 0.8534 (ttp-110) cc_final: 0.7879 (ptp90) REVERT: 5 103 LYS cc_start: 0.9031 (mmmt) cc_final: 0.8543 (mmtm) REVERT: 7 27 GLN cc_start: 0.8564 (mp10) cc_final: 0.8340 (mp10) REVERT: 7 48 TYR cc_start: 0.8756 (p90) cc_final: 0.8527 (p90) REVERT: A 530 MET cc_start: 0.7611 (mmp) cc_final: 0.7135 (mmp) REVERT: A 588 ARG cc_start: 0.9063 (mtt180) cc_final: 0.8529 (ttm110) REVERT: A 589 ASP cc_start: 0.8818 (m-30) cc_final: 0.8541 (m-30) REVERT: A 632 ASP cc_start: 0.8954 (t70) cc_final: 0.8690 (t70) REVERT: C 45 TRP cc_start: 0.8996 (p90) cc_final: 0.8305 (p90) REVERT: C 46 LYS cc_start: 0.9320 (tptt) cc_final: 0.9074 (tppt) REVERT: C 140 ASP cc_start: 0.7971 (m-30) cc_final: 0.7426 (t0) REVERT: C 161 MET cc_start: 0.9337 (tpp) cc_final: 0.8693 (tpp) REVERT: C 425 ASN cc_start: 0.8915 (t0) cc_final: 0.8490 (t0) REVERT: C 492 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8313 (mp0) REVERT: D 574 LYS cc_start: 0.9383 (ptpt) cc_final: 0.9003 (pttp) REVERT: H 55 GLU cc_start: 0.5434 (mm-30) cc_final: 0.5070 (mm-30) REVERT: L 4 MET cc_start: 0.4077 (mmm) cc_final: 0.3801 (mtp) REVERT: L 92 PHE cc_start: 0.8396 (t80) cc_final: 0.8064 (t80) REVERT: M 100 LYS cc_start: 0.9512 (mmmm) cc_final: 0.8592 (tmtt) REVERT: M 100 MET cc_start: 0.7472 (mmm) cc_final: 0.6881 (mmm) REVERT: M 103 LYS cc_start: 0.8827 (mmmt) cc_final: 0.8311 (mmtm) REVERT: M 105 THR cc_start: 0.8066 (m) cc_final: 0.7796 (p) REVERT: Q 72 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8702 (tp-100) REVERT: Q 89 GLU cc_start: 0.6871 (tm-30) cc_final: 0.6626 (tm-30) REVERT: Q 105 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8991 (pp30) REVERT: R 32 MET cc_start: 0.8872 (tpt) cc_final: 0.8625 (tpt) REVERT: R 33 THR cc_start: 0.8890 (m) cc_final: 0.8594 (m) REVERT: R 46 LEU cc_start: 0.9210 (mp) cc_final: 0.8900 (mp) REVERT: c 45 TRP cc_start: 0.9016 (p90) cc_final: 0.8687 (p90) REVERT: c 83 GLU cc_start: 0.8857 (pt0) cc_final: 0.8321 (pm20) REVERT: c 100 MET cc_start: 0.9197 (ptt) cc_final: 0.8606 (ppp) REVERT: c 123 THR cc_start: 0.9206 (p) cc_final: 0.8765 (t) REVERT: c 140 ASP cc_start: 0.7437 (m-30) cc_final: 0.6780 (t70) REVERT: c 321 ASP cc_start: 0.8433 (t0) cc_final: 0.8174 (t0) REVERT: c 434 MET cc_start: 0.7782 (ttm) cc_final: 0.7360 (mtp) REVERT: c 492 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8352 (mp0) REVERT: d 530 MET cc_start: 0.7814 (mmp) cc_final: 0.7248 (mmp) REVERT: d 574 LYS cc_start: 0.9063 (pttp) cc_final: 0.8762 (pttm) REVERT: d 575 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8597 (tm-30) REVERT: d 588 ARG cc_start: 0.9056 (mtt180) cc_final: 0.8709 (ttm-80) REVERT: d 589 ASP cc_start: 0.8878 (m-30) cc_final: 0.8585 (m-30) REVERT: d 655 LYS cc_start: 0.9382 (mmmm) cc_final: 0.8958 (pttp) REVERT: h 31 ARG cc_start: 0.8926 (ttm170) cc_final: 0.8448 (mmt-90) REVERT: h 81 ARG cc_start: 0.8793 (ttp-110) cc_final: 0.8333 (mtt90) REVERT: l 4 MET cc_start: 0.3921 (mmm) cc_final: 0.3691 (mtp) REVERT: m 100 LYS cc_start: 0.9491 (mmmm) cc_final: 0.8613 (tmtt) REVERT: n 30 SER cc_start: 0.9294 (m) cc_final: 0.8701 (p) REVERT: q 28 ASN cc_start: 0.8937 (t0) cc_final: 0.8563 (t0) REVERT: q 52 LYS cc_start: 0.9415 (mtmm) cc_final: 0.8741 (mtmm) REVERT: r 32 MET cc_start: 0.8897 (tpt) cc_final: 0.8663 (tpt) outliers start: 1 outliers final: 0 residues processed: 450 average time/residue: 0.2018 time to fit residues: 143.0461 Evaluate side-chains 358 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 166 optimal weight: 2.9990 chunk 122 optimal weight: 0.0970 chunk 138 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 324 optimal weight: 7.9990 chunk 312 optimal weight: 0.3980 chunk 333 optimal weight: 1.9990 chunk 266 optimal weight: 0.0980 chunk 146 optimal weight: 0.0070 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 42 GLN 7 36 GLN ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 105 GLN d 543 ASN ** d 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 37 GLN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.090971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.064072 restraints weight = 124149.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066428 restraints weight = 65516.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.067969 restraints weight = 43312.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.068985 restraints weight = 32856.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.069590 restraints weight = 27413.646| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32778 Z= 0.121 Angle : 0.704 14.388 44787 Z= 0.343 Chirality : 0.045 0.225 5322 Planarity : 0.005 0.075 5454 Dihedral : 5.023 42.595 4149 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.03 % Allowed : 0.33 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.14), residues: 3786 helix: 0.83 (0.27), residues: 417 sheet: -0.52 (0.14), residues: 1248 loop : -1.21 (0.14), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 542 TYR 0.021 0.001 TYR 3 99 PHE 0.019 0.001 PHE c 53 TRP 0.031 0.001 TRP m 34 HIS 0.005 0.001 HIS 2 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (32598) covalent geometry : angle 0.67940 / 0.34 (44292) SS BOND : bond 0.00201 / 0.12 ( 45) SS BOND : angle 1.56771 / 1.05 ( 90) hydrogen bonds : bond 0.03298 / 2.18 ( 1043) hydrogen bonds : angle 5.25004 / 3.58 ( 2832) link_ALPHA1-2 : bond 0.00588 / 0.31 ( 6) link_ALPHA1-2 : angle 1.58963 / 0.93 ( 18) link_ALPHA1-3 : bond 0.00688 / 0.46 ( 18) link_ALPHA1-3 : angle 1.58539 / 1.09 ( 54) link_ALPHA1-6 : bond 0.00384 / 0.24 ( 9) link_ALPHA1-6 : angle 1.56822 / 0.98 ( 27) link_BETA1-4 : bond 0.00442 / 0.27 ( 57) link_BETA1-4 : angle 2.16820 / 1.53 ( 171) link_NAG-ASN : bond 0.00305 / 0.20 ( 45) link_NAG-ASN : angle 1.87679 / 1.33 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 483 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 45 TRP cc_start: 0.9005 (p90) cc_final: 0.8682 (p90) REVERT: 2 52 LEU cc_start: 0.9419 (mt) cc_final: 0.9162 (mm) REVERT: 2 83 GLU cc_start: 0.8778 (pt0) cc_final: 0.8271 (pm20) REVERT: 2 119 CYS cc_start: 0.6337 (m) cc_final: 0.5891 (m) REVERT: 2 425 ASN cc_start: 0.8565 (t0) cc_final: 0.8040 (t0) REVERT: 2 426 MET cc_start: 0.8423 (ptm) cc_final: 0.7964 (ptm) REVERT: 2 492 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8510 (mm-30) REVERT: 3 31 ASP cc_start: 0.7292 (t0) cc_final: 0.6974 (m-30) REVERT: 3 51 MET cc_start: 0.1554 (ttp) cc_final: 0.1072 (ttm) REVERT: 3 55 GLU cc_start: 0.5831 (mm-30) cc_final: 0.5410 (mm-30) REVERT: 3 81 ARG cc_start: 0.8576 (ttp-110) cc_final: 0.7943 (ptp90) REVERT: 4 4 MET cc_start: 0.5003 (ptp) cc_final: 0.2018 (mtt) REVERT: 5 100 LYS cc_start: 0.9545 (mmmm) cc_final: 0.9099 (tppt) REVERT: 5 103 LYS cc_start: 0.9063 (mmmt) cc_final: 0.8621 (mmtm) REVERT: 7 27 GLN cc_start: 0.8561 (mp10) cc_final: 0.8329 (mp10) REVERT: 7 78 ASP cc_start: 0.9429 (t70) cc_final: 0.9125 (t70) REVERT: 8 30 ARG cc_start: 0.8969 (mtt90) cc_final: 0.8739 (mtt90) REVERT: A 530 MET cc_start: 0.7494 (mmp) cc_final: 0.7031 (mmp) REVERT: A 588 ARG cc_start: 0.9013 (mtt180) cc_final: 0.8564 (ttm110) REVERT: A 589 ASP cc_start: 0.8748 (m-30) cc_final: 0.8450 (m-30) REVERT: A 591 GLN cc_start: 0.9503 (tm-30) cc_final: 0.8938 (tm-30) REVERT: A 632 ASP cc_start: 0.8872 (t70) cc_final: 0.8521 (t70) REVERT: A 633 LYS cc_start: 0.9243 (mmmm) cc_final: 0.8681 (mmtm) REVERT: C 45 TRP cc_start: 0.8883 (p90) cc_final: 0.8504 (p90) REVERT: C 112 TRP cc_start: 0.9524 (t-100) cc_final: 0.9323 (t-100) REVERT: C 140 ASP cc_start: 0.7885 (m-30) cc_final: 0.7346 (t0) REVERT: C 161 MET cc_start: 0.9316 (tpp) cc_final: 0.8615 (tpp) REVERT: C 425 ASN cc_start: 0.8885 (t0) cc_final: 0.8451 (t0) REVERT: C 492 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8437 (mm-30) REVERT: D 574 LYS cc_start: 0.9346 (ptpt) cc_final: 0.9079 (pttp) REVERT: D 633 LYS cc_start: 0.9374 (mmmm) cc_final: 0.8950 (mmtm) REVERT: H 55 GLU cc_start: 0.5431 (mm-30) cc_final: 0.5120 (mm-30) REVERT: L 4 MET cc_start: 0.4133 (mmm) cc_final: 0.3712 (mtp) REVERT: L 92 PHE cc_start: 0.8405 (t80) cc_final: 0.8102 (t80) REVERT: M 100 LYS cc_start: 0.9490 (mmmm) cc_final: 0.8567 (tmtt) REVERT: M 100 MET cc_start: 0.7224 (mmm) cc_final: 0.6644 (mmm) REVERT: M 103 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8444 (mmtm) REVERT: M 105 THR cc_start: 0.7907 (m) cc_final: 0.7665 (p) REVERT: Q 89 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6591 (tm-30) REVERT: Q 105 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8973 (pp30) REVERT: R 33 THR cc_start: 0.8774 (m) cc_final: 0.8470 (m) REVERT: R 46 LEU cc_start: 0.9146 (mp) cc_final: 0.8754 (mp) REVERT: c 45 TRP cc_start: 0.8940 (p90) cc_final: 0.8669 (p90) REVERT: c 83 GLU cc_start: 0.8790 (pt0) cc_final: 0.8288 (pm20) REVERT: c 95 MET cc_start: 0.9054 (pmm) cc_final: 0.8823 (pmm) REVERT: c 100 MET cc_start: 0.9027 (ptt) cc_final: 0.8510 (ppp) REVERT: c 123 THR cc_start: 0.9131 (p) cc_final: 0.8660 (t) REVERT: c 321 ASP cc_start: 0.8224 (t0) cc_final: 0.7969 (t0) REVERT: c 425 ASN cc_start: 0.8977 (t0) cc_final: 0.8458 (t0) REVERT: c 492 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8409 (mp0) REVERT: d 530 MET cc_start: 0.7573 (mmp) cc_final: 0.7015 (mmp) REVERT: d 574 LYS cc_start: 0.9052 (pttp) cc_final: 0.8786 (pttm) REVERT: d 588 ARG cc_start: 0.8982 (mtt180) cc_final: 0.8608 (ttm-80) REVERT: d 589 ASP cc_start: 0.8785 (m-30) cc_final: 0.8538 (m-30) REVERT: d 591 GLN cc_start: 0.9478 (pp30) cc_final: 0.9265 (tm-30) REVERT: d 632 ASP cc_start: 0.8669 (t70) cc_final: 0.8456 (t70) REVERT: d 633 LYS cc_start: 0.9148 (mmmm) cc_final: 0.8699 (mmtm) REVERT: d 655 LYS cc_start: 0.9372 (mmmm) cc_final: 0.8966 (pttp) REVERT: h 31 ARG cc_start: 0.8803 (ttm170) cc_final: 0.8428 (mmt-90) REVERT: h 51 MET cc_start: 0.3098 (ttp) cc_final: 0.2534 (ttm) REVERT: h 81 ARG cc_start: 0.8839 (ttp-110) cc_final: 0.8300 (mtt90) REVERT: l 4 MET cc_start: 0.3781 (mmm) cc_final: 0.3426 (mtp) REVERT: m 100 LYS cc_start: 0.9456 (mmmm) cc_final: 0.8620 (tmtt) REVERT: n 30 SER cc_start: 0.9246 (m) cc_final: 0.8681 (p) REVERT: q 23 ARG cc_start: 0.7824 (ttp80) cc_final: 0.7306 (ttp80) REVERT: q 28 ASN cc_start: 0.8839 (t0) cc_final: 0.8614 (t0) REVERT: q 52 LYS cc_start: 0.9412 (mtmm) cc_final: 0.8746 (mtmm) REVERT: r 78 ASP cc_start: 0.9437 (t70) cc_final: 0.9048 (t70) outliers start: 1 outliers final: 0 residues processed: 484 average time/residue: 0.2058 time to fit residues: 156.9791 Evaluate side-chains 383 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 382 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 180 optimal weight: 0.7980 chunk 254 optimal weight: 0.6980 chunk 228 optimal weight: 0.9990 chunk 372 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 132 optimal weight: 0.7980 chunk 190 optimal weight: 8.9990 chunk 300 optimal weight: 0.9990 chunk 367 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 271 optimal weight: 0.0170 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 42 GLN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 105 GLN d 543 ASN ** d 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 37 GLN q 64 GLN ** q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.091016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.063989 restraints weight = 125674.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.066308 restraints weight = 66944.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.067844 restraints weight = 44502.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.068848 restraints weight = 33888.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.069445 restraints weight = 28420.129| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32778 Z= 0.120 Angle : 0.690 14.149 44787 Z= 0.337 Chirality : 0.044 0.225 5322 Planarity : 0.005 0.069 5454 Dihedral : 4.891 33.466 4149 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.14), residues: 3786 helix: 0.77 (0.27), residues: 417 sheet: -0.55 (0.14), residues: 1260 loop : -1.11 (0.14), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 94 TYR 0.037 0.001 TYR A 643 PHE 0.017 0.001 PHE Q 91 TRP 0.022 0.001 TRP m 34 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (32598) covalent geometry : angle 0.66669 / 0.33 (44292) SS BOND : bond 0.00234 / 0.13 ( 45) SS BOND : angle 1.35121 / 0.92 ( 90) hydrogen bonds : bond 0.03307 / 2.19 ( 1043) hydrogen bonds : angle 5.16048 / 3.51 ( 2832) link_ALPHA1-2 : bond 0.00550 / 0.29 ( 6) link_ALPHA1-2 : angle 1.56920 / 0.91 ( 18) link_ALPHA1-3 : bond 0.00652 / 0.43 ( 18) link_ALPHA1-3 : angle 1.60951 / 1.09 ( 54) link_ALPHA1-6 : bond 0.00382 / 0.24 ( 9) link_ALPHA1-6 : angle 1.53335 / 0.97 ( 27) link_BETA1-4 : bond 0.00425 / 0.26 ( 57) link_BETA1-4 : angle 2.14237 / 1.50 ( 171) link_NAG-ASN : bond 0.00309 / 0.20 ( 45) link_NAG-ASN : angle 1.84615 / 1.30 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6534.21 seconds wall clock time: 113 minutes 34.15 seconds (6814.15 seconds total)