Starting phenix.real_space_refine on Mon Sep 14 17:39:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6mph_9189/09_2026/6mph_9189.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mph_9189/09_2026/6mph_9189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6mph_9189/09_2026/6mph_9189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mph_9189/09_2026/6mph_9189.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mph_9189/09_2026/6mph_9189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mph_9189/09_2026/6mph_9189.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6mph_9189/09_2026/6mph_9189.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6mph_9189/09_2026/6mph_9189.cif" } resolution = 3.8 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= 0.014 sd= 0.126 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 165 5.16 5 C 20157 2.51 5 N 5316 2.21 5 O 6454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 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: 32092 Number of models: 1 Model: "" Number of chains: 72 Chain: "1" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "2" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "3" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "4" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "6" 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: "A" 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: "B" 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: "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: "E" 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: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "L" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} 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: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "Q" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} 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: "X" 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: "Y" 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: "Z" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "a" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "f" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "g" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "h" 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: "i" 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: "F" 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: "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: 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: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 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: "b" 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: "c" 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: 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: 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: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 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: "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: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "5" 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: "7" 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: "8" 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: "9" 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: "AA" 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: "BA" 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: "CA" 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: "DA" 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: "6" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.66, per 1000 atoms: 0.21 Number of scatterers: 32092 At special positions: 0 Unit cell: (157.94, 156.88, 152.64, 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 165 16.00 O 6454 8.00 N 5316 7.00 C 20157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS 1 22 " - pdb=" SG CYS 1 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 23 " - pdb=" SG CYS 2 88 " 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 6 598 " - pdb=" SG CYS 6 604 " distance=2.02 Simple disulfide: pdb=" SG CYS 6 605 " - pdb=" SG CYS A 501 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 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 C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 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 103 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 109 " - pdb=" SG CYS Q 112 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.03 Simple disulfide: pdb=" SG CYS a 23 " - pdb=" SG CYS a 88 " distance=2.03 Simple disulfide: pdb=" SG CYS f 22 " - pdb=" SG CYS f 103 " distance=2.03 Simple disulfide: pdb=" SG CYS f 109 " - pdb=" SG CYS f 112 " distance=2.03 Simple disulfide: pdb=" SG CYS g 22 " - pdb=" SG CYS g 103 " distance=2.03 Simple disulfide: pdb=" SG CYS g 109 " - pdb=" SG CYS g 112 " 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 0 4 " - " MAN 0 5 " " MAN S 4 " - " MAN S 5 " " MAN n 4 " - " MAN n 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA 9 3 " - " MAN 9 4 " " BMA F 3 " - " MAN F 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA S 3 " - " MAN S 4 " " BMA W 3 " - " MAN W 4 " " BMA c 3 " - " MAN c 4 " " BMA e 3 " - " MAN e 4 " " BMA j 3 " - " MAN j 4 " " BMA n 3 " - " MAN n 4 " " BMA r 3 " - " MAN r 4 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " " BMA w 3 " - " MAN w 4 " " BMABA 3 " - " MANBA 4 " " BMACA 3 " - " MANCA 4 " " BMADA 3 " - " MANDA 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 6 " " BMA 9 3 " - " MAN 9 5 " " BMA F 3 " - " MAN F 5 " " BMA J 3 " - " MAN J 5 " " BMA S 3 " - " MAN S 6 " " BMA W 3 " - " MAN W 5 " " BMA j 3 " - " MAN j 5 " " BMA n 3 " - " MAN n 6 " " BMA r 3 " - " MAN r 5 " " BMA t 3 " - " MAN t 5 " " BMA w 3 " - " MAN w 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " 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 K 2 " - " BMA K 3 " " 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 U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " NAG-ASN " NAG 5 1 " - " ASN C 295 " " NAG 6 701 " - " ASN 6 637 " " NAG 8 1 " - " ASN C 363 " " NAG 9 1 " - " ASN C 386 " " NAG A 635 " - " ASN A 339 " " NAG A 647 " - " ASN A 88 " " NAG B 634 " - " ASN B 339 " " NAG B 646 " - " ASN B 88 " " NAG C 635 " - " ASN C 339 " " NAG C 647 " - " ASN C 88 " " NAG D 701 " - " ASN D 637 " " NAG E 701 " - " ASN E 637 " " NAG F 1 " - " ASN A 332 " " NAG K 1 " - " ASN A 160 " " NAG T 1 " - " ASN A 295 " " NAG V 1 " - " ASN A 363 " " NAG W 1 " - " ASN A 386 " " NAG b 1 " - " ASN A 392 " " NAG c 1 " - " ASN B 332 " " NAG k 1 " - " ASN B 160 " " NAG o 1 " - " ASN B 295 " " NAG q 1 " - " ASN B 363 " " NAG r 1 " - " ASN B 386 " " NAG s 1 " - " ASN B 392 " " NAG t 1 " - " ASN C 332 " " NAG x 1 " - " ASN C 160 " " NAGAA 1 " - " ASN C 392 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.2 seconds 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7038 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 78 sheets defined 14.5% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain '1' and resid 60 through 64 Processing helix chain '1' and resid 83 through 87 removed outlier: 3.527A pdb=" N THR 1 87 " --> pdb=" O ALA 1 84 " (cutoff:3.500A) Processing helix chain '2' and resid 79 through 83 removed outlier: 3.513A pdb=" N ASP 2 82 " --> pdb=" O GLU 2 79 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL 2 83 " --> pdb=" O ALA 2 80 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 79 through 83' Processing helix chain '3' and resid 60 through 64 Processing helix chain '3' and resid 83 through 87 removed outlier: 3.535A pdb=" N THR 3 87 " --> pdb=" O ALA 3 84 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 83 removed outlier: 3.532A pdb=" N ASP 4 82 " --> pdb=" O GLU 4 79 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL 4 83 " --> pdb=" O ALA 4 80 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 79 through 83' Processing helix chain '6' and resid 529 through 534 Processing helix chain '6' and resid 537 through 543 Processing helix chain '6' and resid 570 through 595 removed outlier: 3.673A pdb=" N LYS 6 574 " --> pdb=" O VAL 6 570 " (cutoff:3.500A) Processing helix chain '6' and resid 611 through 616 removed outlier: 4.107A pdb=" N SER 6 615 " --> pdb=" O ASN 6 611 " (cutoff:3.500A) Processing helix chain '6' and resid 618 through 626 removed outlier: 3.537A pdb=" N ILE 6 622 " --> pdb=" O ASN 6 618 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TRP 6 623 " --> pdb=" O LEU 6 619 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP 6 624 " --> pdb=" O SER 6 620 " (cutoff:3.500A) Processing helix chain '6' and resid 627 through 635 Processing helix chain '6' and resid 641 through 664 Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.690A pdb=" N TYR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.554A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.537A pdb=" N THR A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.807A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 removed outlier: 3.680A pdb=" N TYR B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 removed outlier: 4.184A pdb=" N HIS B 66 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN B 67 " --> pdb=" O GLU B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 63 through 67' Processing helix chain 'B' and resid 100 through 115 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.520A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.832A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.667A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 removed outlier: 4.166A pdb=" N HIS C 66 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN C 67 " --> pdb=" O GLU C 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 63 through 67' Processing helix chain 'C' and resid 100 through 115 Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.605A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix 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 Processing helix chain 'C' and resid 475 through 480 removed outlier: 3.832A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 Processing helix chain 'D' and resid 570 through 595 removed outlier: 3.662A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 616 removed outlier: 4.110A pdb=" N SER D 615 " --> pdb=" O ASN D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.555A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TRP D 623 " --> pdb=" O LEU D 619 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 641 through 664 Processing helix chain 'E' and resid 523 through 527 removed outlier: 3.578A pdb=" N ALA E 526 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 523 through 527' Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 537 through 543 Processing helix chain 'E' and resid 570 through 595 removed outlier: 3.654A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 616 removed outlier: 4.113A pdb=" N SER E 615 " --> pdb=" O ASN E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.551A pdb=" N ILE E 622 " --> pdb=" O ASN E 618 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP E 623 " --> pdb=" O LEU E 619 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP E 624 " --> pdb=" O SER E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 641 through 664 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.553A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.536A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.903A pdb=" N SER M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'Q' and resid 62 through 65 removed outlier: 3.618A pdb=" N GLN Q 65 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 62 through 65' Processing helix chain 'Q' and resid 94 through 98 removed outlier: 3.687A pdb=" N THR Q 98 " --> pdb=" O PRO Q 95 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 87 removed outlier: 3.910A pdb=" N SER X 87 " --> pdb=" O ALA X 84 " (cutoff:3.500A) Processing helix chain 'Y' and resid 83 through 87 removed outlier: 3.936A pdb=" N SER Y 87 " --> pdb=" O ALA Y 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 83 Processing helix chain 'a' and resid 79 through 83 Processing helix chain 'f' and resid 62 through 65 removed outlier: 3.624A pdb=" N GLN f 65 " --> pdb=" O ARG f 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 62 through 65' Processing helix chain 'f' and resid 94 through 98 removed outlier: 3.683A pdb=" N THR f 98 " --> pdb=" O PRO f 95 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 65 removed outlier: 3.662A pdb=" N GLN g 65 " --> pdb=" O ARG g 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 62 through 65' Processing helix chain 'g' and resid 94 through 98 removed outlier: 3.623A pdb=" N THR g 98 " --> pdb=" O PRO g 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain '1' and resid 11 through 12 removed outlier: 3.812A pdb=" N VAL 1 12 " --> pdb=" O THR 1 110 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP 1 34 " --> pdb=" O TYR 1 50 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR 1 50 " --> pdb=" O TRP 1 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP 1 36 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 18 through 19 Processing sheet with id=AA4, first strand: chain '2' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain '2' and resid 45 through 49 removed outlier: 6.569A pdb=" N TRP 2 35 " --> pdb=" O LEU 2 47 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR 2 49 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU 2 33 " --> pdb=" O TYR 2 49 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY 2 84 " --> pdb=" O VAL 2 104 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL 2 104 " --> pdb=" O GLY 2 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain '3' and resid 11 through 12 removed outlier: 3.820A pdb=" N VAL 3 12 " --> pdb=" O THR 3 110 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP 3 34 " --> pdb=" O TYR 3 50 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TYR 3 50 " --> pdb=" O TRP 3 34 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP 3 36 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 18 through 19 Processing sheet with id=AA9, first strand: chain '4' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain '4' and resid 45 through 49 removed outlier: 6.558A pdb=" N TRP 4 35 " --> pdb=" O LEU 4 47 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR 4 49 " --> pdb=" O LEU 4 33 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU 4 33 " --> pdb=" O TYR 4 49 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY 4 84 " --> pdb=" O VAL 4 104 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL 4 104 " --> pdb=" O GLY 4 84 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '6' and resid 603 through 609 removed outlier: 3.542A pdb=" N VAL A 38 " --> pdb=" O CYS 6 604 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR 6 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL A 36 " --> pdb=" O THR 6 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.817A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.759A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AB8, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.927A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.024A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.018A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 271 through 274 removed outlier: 11.018A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.024A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 302 through 312 removed outlier: 6.021A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 495 through 499 removed outlier: 5.149A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR E 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 38 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS E 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AC4, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.799A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.761A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AC7, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AC8, first strand: chain 'B' and resid 260 through 261 removed outlier: 6.950A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.622A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.010A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 271 through 274 removed outlier: 11.010A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 11.622A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER B 393 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 302 through 312 removed outlier: 6.042A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.133A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR D 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 38 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS D 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AD4, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.803A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.779A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AD7, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=AD8, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.945A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.516A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.970A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 271 through 273 removed outlier: 10.970A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.516A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 302 through 312 removed outlier: 6.014A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AE4, first strand: chain 'H' and resid 46 through 52 removed outlier: 6.755A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'L' and resid 45 through 49 removed outlier: 6.559A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL L 104 " --> pdb=" O GLY L 84 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AE8, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.749A pdb=" N THR M 95 " --> pdb=" O TYR M 33 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR M 33 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AF1, first strand: chain 'N' and resid 12 through 13 removed outlier: 3.589A pdb=" N VAL N 13 " --> pdb=" O ILE N 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'N' and resid 19 through 26 removed outlier: 4.135A pdb=" N ALA N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 44 through 48 removed outlier: 6.589A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 3 through 5 Processing sheet with id=AF5, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.610A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY Q 44 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 10 through 12 Processing sheet with id=AF7, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AF8, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.057A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TRP R 34 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.057A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'X' and resid 5 through 7 Processing sheet with id=AG2, first strand: chain 'X' and resid 11 through 12 removed outlier: 3.738A pdb=" N THR X 95 " --> pdb=" O TYR X 33 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR X 33 " --> pdb=" O THR X 95 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP X 34 " --> pdb=" O TYR X 50 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR X 50 " --> pdb=" O TRP X 34 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP X 36 " --> pdb=" O ILE X 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 11 through 12 Processing sheet with id=AG4, first strand: chain 'Y' and resid 5 through 7 Processing sheet with id=AG5, first strand: chain 'Y' and resid 11 through 12 removed outlier: 3.766A pdb=" N THR Y 95 " --> pdb=" O TYR Y 33 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR Y 33 " --> pdb=" O THR Y 95 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP Y 34 " --> pdb=" O TYR Y 50 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR Y 50 " --> pdb=" O TRP Y 34 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TRP Y 36 " --> pdb=" O ILE Y 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 11 through 12 Processing sheet with id=AG7, first strand: chain 'Z' and resid 12 through 13 removed outlier: 3.579A pdb=" N VAL Z 13 " --> pdb=" O ILE Z 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'Z' and resid 19 through 26 removed outlier: 4.067A pdb=" N ALA Z 71 " --> pdb=" O CYS Z 23 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 44 through 48 removed outlier: 6.610A pdb=" N TRP Z 35 " --> pdb=" O ILE Z 47 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'a' and resid 12 through 13 removed outlier: 3.584A pdb=" N VAL a 13 " --> pdb=" O ILE a 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'a' and resid 19 through 26 removed outlier: 4.087A pdb=" N ALA a 71 " --> pdb=" O CYS a 23 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 44 through 48 removed outlier: 6.601A pdb=" N TRP a 35 " --> pdb=" O ILE a 47 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'f' and resid 3 through 5 Processing sheet with id=AH5, first strand: chain 'f' and resid 10 through 12 removed outlier: 6.564A pdb=" N ILE f 34 " --> pdb=" O TRP f 50 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TRP f 50 " --> pdb=" O ILE f 34 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP f 36 " --> pdb=" O ILE f 48 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY f 44 " --> pdb=" O ILE f 40 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'f' and resid 10 through 12 Processing sheet with id=AH7, first strand: chain 'g' and resid 3 through 5 Processing sheet with id=AH8, first strand: chain 'g' and resid 10 through 12 removed outlier: 6.563A pdb=" N ILE g 34 " --> pdb=" O TRP g 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP g 50 " --> pdb=" O ILE g 34 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP g 36 " --> pdb=" O ILE g 48 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'g' and resid 10 through 12 Processing sheet with id=AI1, first strand: chain 'h' and resid 5 through 6 Processing sheet with id=AI2, first strand: chain 'h' and resid 10 through 13 removed outlier: 6.054A pdb=" N LEU h 11 " --> pdb=" O GLU h 105 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP h 34 " --> pdb=" O LEU h 47 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'h' and resid 10 through 13 removed outlier: 6.054A pdb=" N LEU h 11 " --> pdb=" O GLU h 105 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'i' and resid 5 through 6 Processing sheet with id=AI5, first strand: chain 'i' and resid 10 through 13 removed outlier: 6.043A pdb=" N LEU i 11 " --> pdb=" O GLU i 105 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TRP i 34 " --> pdb=" O LEU i 47 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'i' and resid 10 through 13 removed outlier: 6.043A pdb=" N LEU i 11 " --> pdb=" O GLU i 105 " (cutoff:3.500A) 1130 hydrogen bonds defined for protein. 2817 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: 7.25 Time building geometry restraints manager: 3.36 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: 9634 1.34 - 1.46: 7150 1.46 - 1.57: 15811 1.57 - 1.69: 1 1.69 - 1.81: 216 Bond restraints: 32812 Sorted by residual: bond pdb=" C1 NAG B 646 " pdb=" O5 NAG B 646 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C1 NAG C 647 " pdb=" O5 NAG C 647 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C1 MAN t 4 " pdb=" C2 MAN t 4 " ideal model delta sigma weight residual 1.526 1.581 -0.055 2.00e-02 2.50e+03 7.60e+00 bond pdb=" C1 MAN v 4 " pdb=" O5 MAN v 4 " ideal model delta sigma weight residual 1.399 1.454 -0.055 2.00e-02 2.50e+03 7.56e+00 bond pdb=" C1 MAN e 4 " pdb=" O5 MAN e 4 " ideal model delta sigma weight residual 1.399 1.454 -0.055 2.00e-02 2.50e+03 7.50e+00 ... (remaining 32807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 43908 3.04 - 6.08: 584 6.08 - 9.11: 121 9.11 - 12.15: 3 12.15 - 15.19: 3 Bond angle restraints: 44619 Sorted by residual: angle pdb=" C ASN A 332 " pdb=" N VAL A 333 " pdb=" CA VAL A 333 " ideal model delta sigma weight residual 122.11 128.03 -5.92 1.12e+00 7.97e-01 2.79e+01 angle pdb=" CA LEU C 494 " pdb=" CB LEU C 494 " pdb=" CG LEU C 494 " ideal model delta sigma weight residual 116.30 131.49 -15.19 3.50e+00 8.16e-02 1.88e+01 angle pdb=" N PHE f 115 " pdb=" CA PHE f 115 " pdb=" C PHE f 115 " ideal model delta sigma weight residual 109.81 119.38 -9.57 2.21e+00 2.05e-01 1.87e+01 angle pdb=" N PHE Q 115 " pdb=" CA PHE Q 115 " pdb=" C PHE Q 115 " ideal model delta sigma weight residual 109.81 119.27 -9.46 2.21e+00 2.05e-01 1.83e+01 angle pdb=" CA LEU B 494 " pdb=" CB LEU B 494 " pdb=" CG LEU B 494 " ideal model delta sigma weight residual 116.30 131.27 -14.97 3.50e+00 8.16e-02 1.83e+01 ... (remaining 44614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 16974 17.71 - 35.42: 1004 35.42 - 53.13: 262 53.13 - 70.84: 40 70.84 - 88.55: 11 Dihedral angle restraints: 18291 sinusoidal: 7299 harmonic: 10992 Sorted by residual: dihedral pdb=" CA GLN L 50 " pdb=" C GLN L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta harmonic sigma weight residual 180.00 -137.35 -42.65 0 5.00e+00 4.00e-02 7.28e+01 dihedral pdb=" CA GLN 4 50 " pdb=" C GLN 4 50 " pdb=" N VAL 4 51 " pdb=" CA VAL 4 51 " ideal model delta harmonic sigma weight residual -180.00 -137.41 -42.59 0 5.00e+00 4.00e-02 7.26e+01 dihedral pdb=" CA GLN 2 50 " pdb=" C GLN 2 50 " pdb=" N VAL 2 51 " pdb=" CA VAL 2 51 " ideal model delta harmonic sigma weight residual -180.00 -137.76 -42.24 0 5.00e+00 4.00e-02 7.14e+01 ... (remaining 18288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 5033 0.110 - 0.220: 295 0.220 - 0.330: 40 0.330 - 0.441: 0 0.441 - 0.551: 3 Chirality restraints: 5371 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.08e+01 chirality pdb=" C1 NAG s 1 " pdb=" ND2 ASN B 392 " pdb=" C2 NAG s 1 " pdb=" O5 NAG s 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.58e+00 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN A 392 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.36e+00 ... (remaining 5368 not shown) Planarity restraints: 5490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE Q 115 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.13e+00 pdb=" N PRO Q 116 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO Q 116 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO Q 116 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE g 115 " 0.050 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO g 116 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO g 116 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO g 116 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE f 115 " -0.048 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO f 116 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO f 116 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO f 116 " -0.041 5.00e-02 4.00e+02 ... (remaining 5487 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9327 2.81 - 3.33: 26640 3.33 - 3.85: 54080 3.85 - 4.38: 59156 4.38 - 4.90: 102943 Nonbonded interactions: 252146 Sorted by model distance: nonbonded pdb=" OG1 THR B 373 " pdb=" N HIS B 374 " model vdw 2.286 3.120 nonbonded pdb=" OG1 THR C 373 " pdb=" N HIS C 374 " model vdw 2.290 3.120 nonbonded pdb=" OG1 THR A 373 " pdb=" N HIS A 374 " model vdw 2.294 3.120 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP g 79 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR B 318 " pdb=" OD2 ASP Q 79 " model vdw 2.314 3.040 ... (remaining 252141 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: 0.08 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'S' selection = chain 'n' } ncs_group { reference = chain '1' selection = chain '3' selection = chain 'H' } ncs_group { reference = chain '2' selection = chain '4' selection = chain 'L' } ncs_group { reference = chain '5' selection = chain '7' selection = chain 'G' selection = chain 'O' selection = chain 'T' selection = chain 'U' selection = chain 'd' selection = chain 'l' selection = chain 'o' selection = chain 'p' selection = chain 'u' selection = chain 'y' } ncs_group { reference = chain '6' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain '8' selection = chain 'AA' selection = chain 'K' selection = chain 'P' selection = chain 'V' selection = chain 'b' selection = chain 'k' selection = chain 'm' selection = chain 'q' selection = chain 's' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain '9' selection = chain 'F' selection = chain 'J' selection = chain 'W' selection = chain 'j' selection = chain 'r' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'BA' selection = chain 'CA' selection = chain 'DA' selection = chain 'I' selection = chain 'c' selection = chain 'e' selection = chain 'v' } ncs_group { reference = chain 'M' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'N' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'Q' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'R' selection = chain 'h' selection = chain 'i' } 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: 3.810 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: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 28.060 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 32997 Z= 0.320 Angle : 0.979 15.191 45120 Z= 0.466 Chirality : 0.059 0.551 5371 Planarity : 0.006 0.076 5463 Dihedral : 12.375 88.553 11091 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.27 % Favored : 94.57 % Rotamer: Outliers : 6.01 % Allowed : 7.18 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -3.46 (0.11), residues: 3777 helix: -2.59 (0.18), residues: 429 sheet: -1.79 (0.13), residues: 1239 loop : -2.59 (0.11), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 503 TYR 0.016 0.002 TYR f 87 PHE 0.025 0.002 PHE C 288 TRP 0.020 0.002 TRP A 96 HIS 0.008 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.32 (32812) covalent geometry : angle 0.92611 / 0.45 (44619) SS BOND : bond 0.00398 / 0.24 ( 54) SS BOND : angle 1.23976 / 0.88 ( 108) hydrogen bonds : bond 0.12858 / 8.42 ( 1064) hydrogen bonds : angle 7.70509 / 5.36 ( 2817) link_ALPHA1-2 : bond 0.00316 / 0.16 ( 3) link_ALPHA1-2 : angle 1.64334 / 0.93 ( 9) link_ALPHA1-3 : bond 0.00508 / 0.33 ( 18) link_ALPHA1-3 : angle 1.64684 / 1.12 ( 54) link_ALPHA1-6 : bond 0.00293 / 0.17 ( 11) link_ALPHA1-6 : angle 1.76889 / 1.14 ( 33) link_BETA1-4 : bond 0.00822 / 0.54 ( 72) link_BETA1-4 : angle 3.78145 / 2.63 ( 216) link_NAG-ASN : bond 0.00950 / 0.64 ( 27) link_NAG-ASN : angle 4.21957 / 2.76 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 615 time to evaluate : 1.340 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: 1 70 LEU cc_start: 0.9177 (mt) cc_final: 0.8878 (mp) REVERT: 1 94 ARG cc_start: 0.8316 (tmm160) cc_final: 0.7868 (ttp80) REVERT: 2 3 VAL cc_start: 0.9238 (t) cc_final: 0.9021 (p) REVERT: 3 94 ARG cc_start: 0.8119 (tmm160) cc_final: 0.7496 (ttp80) REVERT: 4 3 VAL cc_start: 0.9281 (t) cc_final: 0.9040 (p) REVERT: 4 5 THR cc_start: 0.8265 (m) cc_final: 0.8022 (p) REVERT: 6 535 MET cc_start: 0.8557 (mmt) cc_final: 0.8334 (tpp) REVERT: 6 584 GLU cc_start: 0.8558 (tt0) cc_final: 0.8355 (tt0) REVERT: 6 601 LYS cc_start: 0.8698 (mttt) cc_final: 0.8393 (ttpp) REVERT: 6 657 GLU cc_start: 0.9312 (tt0) cc_final: 0.9027 (tm-30) REVERT: 6 659 ASP cc_start: 0.9201 (t0) cc_final: 0.8893 (m-30) REVERT: A 37 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.8854 (p) REVERT: A 138 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8106 (tp) REVERT: A 475 MET cc_start: 0.8890 (mmm) cc_final: 0.8668 (mmm) REVERT: A 494 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8837 (pt) REVERT: B 138 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8081 (tp) REVERT: B 475 MET cc_start: 0.8937 (mmm) cc_final: 0.8706 (mmm) REVERT: C 138 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8236 (tp) REVERT: C 494 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8892 (pt) REVERT: D 543 ASN cc_start: 0.8952 (m-40) cc_final: 0.8721 (t0) REVERT: D 595 ILE cc_start: 0.9298 (pt) cc_final: 0.8796 (pt) REVERT: D 629 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9197 (mp) REVERT: D 633 LYS cc_start: 0.9579 (mttt) cc_final: 0.9372 (mtmm) REVERT: D 651 ASN cc_start: 0.9245 (t0) cc_final: 0.8917 (p0) REVERT: D 657 GLU cc_start: 0.9225 (tt0) cc_final: 0.9024 (tm-30) REVERT: D 659 ASP cc_start: 0.9182 (t0) cc_final: 0.8954 (m-30) REVERT: E 601 LYS cc_start: 0.8743 (mttt) cc_final: 0.8413 (ttpp) REVERT: E 629 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.8942 (mt) REVERT: E 633 LYS cc_start: 0.9554 (mttt) cc_final: 0.9354 (mtmm) REVERT: E 638 TYR cc_start: 0.8507 (m-80) cc_final: 0.7995 (m-10) REVERT: E 659 ASP cc_start: 0.9245 (t0) cc_final: 0.8935 (m-30) REVERT: H 94 ARG cc_start: 0.8402 (tmm160) cc_final: 0.7727 (ttp80) REVERT: L 3 VAL cc_start: 0.9215 (t) cc_final: 0.8976 (p) REVERT: N 54 ARG cc_start: 0.8622 (ptt-90) cc_final: 0.8349 (ptt90) REVERT: N 62 PHE cc_start: 0.8457 (m-80) cc_final: 0.8241 (m-10) REVERT: N 67 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9042 (p) REVERT: R 10 ILE cc_start: 0.9511 (mt) cc_final: 0.9291 (mm) REVERT: X 82 VAL cc_start: 0.8783 (t) cc_final: 0.8366 (t) REVERT: Y 100 LYS cc_start: 0.9500 (mptt) cc_final: 0.9274 (mmmm) REVERT: Z 54 ARG cc_start: 0.8554 (ptt-90) cc_final: 0.8353 (ptm160) REVERT: Z 67 THR cc_start: 0.9438 (OUTLIER) cc_final: 0.9030 (p) REVERT: a 28 LEU cc_start: 0.9182 (mp) cc_final: 0.8903 (mp) REVERT: a 54 ARG cc_start: 0.8574 (ptt-90) cc_final: 0.8253 (ptt90) REVERT: a 67 THR cc_start: 0.9416 (OUTLIER) cc_final: 0.8897 (p) REVERT: f 32 TYR cc_start: 0.9004 (m-80) cc_final: 0.8779 (m-10) REVERT: h 10 ILE cc_start: 0.9523 (mt) cc_final: 0.9299 (mm) REVERT: h 32 MET cc_start: 0.8551 (tpp) cc_final: 0.8053 (tpp) REVERT: h 50 ASP cc_start: 0.8858 (t0) cc_final: 0.8331 (t0) REVERT: h 51 THR cc_start: 0.9563 (OUTLIER) cc_final: 0.9344 (p) REVERT: h 70 ASP cc_start: 0.8929 (m-30) cc_final: 0.8418 (m-30) REVERT: h 104 LEU cc_start: 0.8666 (tp) cc_final: 0.8449 (mt) REVERT: i 32 MET cc_start: 0.8364 (tpp) cc_final: 0.7110 (tpp) REVERT: i 104 LEU cc_start: 0.8482 (tp) cc_final: 0.8149 (mt) outliers start: 200 outliers final: 45 residues processed: 797 average time/residue: 0.2515 time to fit residues: 304.8869 Evaluate side-chains 377 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 320 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain f residue 37 VAL Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain h residue 51 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.0570 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 5.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 58 ASN 1 65 ASN 2 38 GLN 3 58 ASN 3 65 ASN 4 38 GLN 6 577 GLN 6 611 ASN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN A 203 GLN A 287 GLN ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN B 203 GLN B 287 GLN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 203 GLN C 287 GLN D 577 GLN D 611 ASN E 577 GLN E 611 ASN H 58 ASN H 65 ASN L 38 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN ** X 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 32 ASN ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 6 GLN f 118 GLN g 6 GLN g 118 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.063758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.044830 restraints weight = 147656.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.046436 restraints weight = 72031.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.047458 restraints weight = 47508.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.048088 restraints weight = 37178.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.048419 restraints weight = 32184.746| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32997 Z= 0.151 Angle : 0.736 14.803 45120 Z= 0.357 Chirality : 0.046 0.376 5371 Planarity : 0.005 0.061 5463 Dihedral : 6.982 58.668 4233 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.16 % Allowed : 13.56 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.59 (0.12), residues: 3777 helix: -0.80 (0.24), residues: 399 sheet: -1.47 (0.13), residues: 1251 loop : -2.09 (0.12), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG h 39 TYR 0.019 0.001 TYR Z 49 PHE 0.018 0.002 PHE 1 107 TRP 0.016 0.001 TRP 1 54 HIS 0.009 0.001 HIS M 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (32812) covalent geometry : angle 0.70382 / 0.35 (44619) SS BOND : bond 0.00612 / 0.32 ( 54) SS BOND : angle 0.86109 / 0.60 ( 108) hydrogen bonds : bond 0.03675 / 2.35 ( 1064) hydrogen bonds : angle 6.64256 / 4.62 ( 2817) link_ALPHA1-2 : bond 0.00623 / 0.31 ( 3) link_ALPHA1-2 : angle 1.46788 / 0.90 ( 9) link_ALPHA1-3 : bond 0.00786 / 0.52 ( 18) link_ALPHA1-3 : angle 1.60008 / 1.08 ( 54) link_ALPHA1-6 : bond 0.00362 / 0.21 ( 11) link_ALPHA1-6 : angle 1.53377 / 1.02 ( 33) link_BETA1-4 : bond 0.00551 / 0.37 ( 72) link_BETA1-4 : angle 2.29722 / 1.59 ( 216) link_NAG-ASN : bond 0.00517 / 0.33 ( 27) link_NAG-ASN : angle 3.25757 / 2.14 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 403 time to evaluate : 1.250 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: 1 76 ASN cc_start: 0.8980 (t0) cc_final: 0.8685 (t0) REVERT: 1 94 ARG cc_start: 0.8039 (tmm160) cc_final: 0.7649 (ttp80) REVERT: 2 24 ARG cc_start: 0.9040 (mtt90) cc_final: 0.8726 (mmt90) REVERT: 2 45 ARG cc_start: 0.8956 (tpm170) cc_final: 0.8574 (tpm170) REVERT: 4 24 ARG cc_start: 0.9057 (mtt90) cc_final: 0.8816 (mmt90) REVERT: 6 571 TRP cc_start: 0.7163 (m-90) cc_final: 0.6672 (m-10) REVERT: 6 574 LYS cc_start: 0.8699 (ptmt) cc_final: 0.8399 (ptpp) REVERT: 6 659 ASP cc_start: 0.9193 (t0) cc_final: 0.8839 (m-30) REVERT: B 125 LEU cc_start: 0.9622 (tp) cc_final: 0.9270 (tp) REVERT: B 475 MET cc_start: 0.8815 (mmm) cc_final: 0.8608 (mmm) REVERT: C 114 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8686 (tm-30) REVERT: D 595 ILE cc_start: 0.9247 (pt) cc_final: 0.9023 (pt) REVERT: D 629 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9229 (mp) REVERT: D 647 GLU cc_start: 0.8792 (tp30) cc_final: 0.8074 (mm-30) REVERT: D 651 ASN cc_start: 0.9322 (t0) cc_final: 0.8961 (p0) REVERT: D 659 ASP cc_start: 0.9157 (t0) cc_final: 0.8884 (m-30) REVERT: E 581 LEU cc_start: 0.9589 (tp) cc_final: 0.9297 (tt) REVERT: E 601 LYS cc_start: 0.8768 (mttt) cc_final: 0.8326 (ttpp) REVERT: E 629 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9071 (mt) REVERT: E 638 TYR cc_start: 0.8495 (m-80) cc_final: 0.8014 (m-10) REVERT: E 659 ASP cc_start: 0.9128 (t0) cc_final: 0.8872 (m-30) REVERT: H 94 ARG cc_start: 0.8069 (tmm160) cc_final: 0.7564 (ttp80) REVERT: M 23 ASN cc_start: 0.8766 (t0) cc_final: 0.8490 (t0) REVERT: M 100 MET cc_start: 0.8952 (mpp) cc_final: 0.8576 (mpp) REVERT: N 47 ILE cc_start: 0.9277 (pt) cc_final: 0.8832 (mt) REVERT: N 54 ARG cc_start: 0.8619 (ptt-90) cc_final: 0.8315 (ptt90) REVERT: N 67 THR cc_start: 0.9499 (OUTLIER) cc_final: 0.9062 (p) REVERT: N 96 TRP cc_start: 0.8020 (m100) cc_final: 0.7595 (m100) REVERT: Q 118 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8570 (tm-30) REVERT: R 37 GLN cc_start: 0.9151 (tt0) cc_final: 0.8864 (tm-30) REVERT: R 70 ASP cc_start: 0.8943 (m-30) cc_final: 0.8728 (p0) REVERT: X 23 ASN cc_start: 0.8686 (t0) cc_final: 0.8392 (t0) REVERT: X 64 LYS cc_start: 0.9064 (tppt) cc_final: 0.8576 (tppt) REVERT: X 100 MET cc_start: 0.8938 (mpp) cc_final: 0.8255 (mmm) REVERT: Y 23 ASN cc_start: 0.8987 (t0) cc_final: 0.8679 (t0) REVERT: Y 53 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7259 (p0) REVERT: Z 96 TRP cc_start: 0.8110 (m100) cc_final: 0.7527 (m100) REVERT: Z 100 GLU cc_start: 0.8425 (pm20) cc_final: 0.8185 (pm20) REVERT: a 28 LEU cc_start: 0.9102 (mp) cc_final: 0.8887 (mp) REVERT: a 67 THR cc_start: 0.9449 (OUTLIER) cc_final: 0.9071 (p) REVERT: a 96 TRP cc_start: 0.7919 (m100) cc_final: 0.7583 (m100) REVERT: g 111 TYR cc_start: 0.8717 (m-80) cc_final: 0.8152 (m-80) REVERT: h 1 GLU cc_start: 0.7375 (pt0) cc_final: 0.6860 (mp0) REVERT: h 32 MET cc_start: 0.8359 (tpp) cc_final: 0.7856 (tpp) REVERT: h 70 ASP cc_start: 0.9075 (m-30) cc_final: 0.8868 (p0) REVERT: i 32 MET cc_start: 0.7914 (tpp) cc_final: 0.7444 (tpp) outliers start: 105 outliers final: 57 residues processed: 497 average time/residue: 0.2396 time to fit residues: 184.3619 Evaluate side-chains 379 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 317 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 513 VAL Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 538 THR Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 639 THR Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 604 CYS Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain h residue 63 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 120 optimal weight: 5.9990 chunk 370 optimal weight: 8.9990 chunk 319 optimal weight: 2.9990 chunk 365 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 329 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 231 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 300 optimal weight: 8.9990 chunk 283 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 30AHIS ** 2 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 30AHIS ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN A 156 ASN ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 293 GLN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 293 GLN D 575 GLN E 575 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30AHIS ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN M 5 GLN ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.060367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.041373 restraints weight = 151403.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.042843 restraints weight = 75574.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.043784 restraints weight = 50693.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.044343 restraints weight = 40088.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.044682 restraints weight = 35089.860| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 32997 Z= 0.391 Angle : 0.864 11.984 45120 Z= 0.415 Chirality : 0.048 0.342 5371 Planarity : 0.005 0.056 5463 Dihedral : 6.840 57.146 4200 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.69 % Allowed : 13.59 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.25 (0.13), residues: 3777 helix: -0.25 (0.24), residues: 420 sheet: -1.32 (0.14), residues: 1227 loop : -1.87 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 3 94 TYR 0.019 0.002 TYR D 638 PHE 0.031 0.003 PHE g 115 TRP 0.018 0.002 TRP B 96 HIS 0.008 0.002 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00854 / 0.39 (32812) covalent geometry : angle 0.83003 / 0.41 (44619) SS BOND : bond 0.00543 / 0.33 ( 54) SS BOND : angle 1.27476 / 0.84 ( 108) hydrogen bonds : bond 0.03969 / 2.56 ( 1064) hydrogen bonds : angle 6.52751 / 4.53 ( 2817) link_ALPHA1-2 : bond 0.00310 / 0.15 ( 3) link_ALPHA1-2 : angle 1.64107 / 1.05 ( 9) link_ALPHA1-3 : bond 0.00631 / 0.42 ( 18) link_ALPHA1-3 : angle 1.96260 / 1.33 ( 54) link_ALPHA1-6 : bond 0.00225 / 0.12 ( 11) link_ALPHA1-6 : angle 1.59918 / 1.03 ( 33) link_BETA1-4 : bond 0.00516 / 0.34 ( 72) link_BETA1-4 : angle 2.51431 / 1.71 ( 216) link_NAG-ASN : bond 0.00935 / 0.57 ( 27) link_NAG-ASN : angle 3.68926 / 2.42 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 301 time to evaluate : 1.264 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: 1 94 ARG cc_start: 0.8008 (tmm160) cc_final: 0.7620 (ttp80) REVERT: 2 45 ARG cc_start: 0.9048 (tpm170) cc_final: 0.8678 (tpm170) REVERT: 6 601 LYS cc_start: 0.9004 (mttt) cc_final: 0.8533 (ttpp) REVERT: 6 659 ASP cc_start: 0.9036 (t0) cc_final: 0.8827 (m-30) REVERT: A 100 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.8962 (ptp) REVERT: B 475 MET cc_start: 0.8922 (mmm) cc_final: 0.8535 (mmm) REVERT: B 480 ARG cc_start: 0.9463 (OUTLIER) cc_final: 0.8245 (mtm110) REVERT: D 584 GLU cc_start: 0.8764 (tt0) cc_final: 0.8506 (tm-30) REVERT: D 601 LYS cc_start: 0.8930 (mttt) cc_final: 0.8672 (ttmm) REVERT: D 647 GLU cc_start: 0.8733 (tp30) cc_final: 0.8533 (mm-30) REVERT: D 659 ASP cc_start: 0.9109 (t0) cc_final: 0.8854 (m-30) REVERT: E 584 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8125 (tm-30) REVERT: E 601 LYS cc_start: 0.8956 (mttt) cc_final: 0.8690 (ttmm) REVERT: E 659 ASP cc_start: 0.9159 (t0) cc_final: 0.8791 (m-30) REVERT: H 3 GLN cc_start: 0.9190 (mt0) cc_final: 0.8967 (mm110) REVERT: H 13 ARG cc_start: 0.8880 (tpp80) cc_final: 0.8675 (tpp80) REVERT: H 94 ARG cc_start: 0.8109 (tmm160) cc_final: 0.7494 (ttp80) REVERT: M 100 MET cc_start: 0.9038 (mpp) cc_final: 0.8734 (mmm) REVERT: N 12 SER cc_start: 0.7125 (OUTLIER) cc_final: 0.6904 (m) REVERT: N 47 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.8904 (mm) REVERT: N 54 ARG cc_start: 0.8615 (ptt-90) cc_final: 0.8232 (ptt90) REVERT: N 67 THR cc_start: 0.9464 (OUTLIER) cc_final: 0.8978 (p) REVERT: Q 3 GLN cc_start: 0.8210 (mp10) cc_final: 0.7650 (mp10) REVERT: Q 118 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8725 (tm-30) REVERT: R 70 ASP cc_start: 0.9029 (m-30) cc_final: 0.8795 (p0) REVERT: X 30 ARG cc_start: 0.8794 (tpp80) cc_final: 0.8138 (tpp80) REVERT: X 44 GLN cc_start: 0.8343 (pp30) cc_final: 0.8023 (pp30) REVERT: X 53 ASP cc_start: 0.8100 (p0) cc_final: 0.7338 (p0) REVERT: X 100 MET cc_start: 0.9024 (mpp) cc_final: 0.8224 (mmm) REVERT: Y 30 ARG cc_start: 0.8773 (tpp80) cc_final: 0.8229 (tpp80) REVERT: Y 53 ASP cc_start: 0.7938 (p0) cc_final: 0.7274 (p0) REVERT: Y 64 LYS cc_start: 0.9103 (tppt) cc_final: 0.8683 (tppt) REVERT: Y 100 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8230 (mt-10) REVERT: Z 67 THR cc_start: 0.9441 (OUTLIER) cc_final: 0.8958 (p) REVERT: a 67 THR cc_start: 0.9414 (OUTLIER) cc_final: 0.8999 (p) REVERT: f 32 TYR cc_start: 0.9035 (m-10) cc_final: 0.8820 (m-10) REVERT: f 111 TYR cc_start: 0.8773 (m-80) cc_final: 0.8572 (m-80) REVERT: g 111 TYR cc_start: 0.8824 (m-80) cc_final: 0.8320 (m-80) REVERT: h 32 MET cc_start: 0.8688 (tpp) cc_final: 0.8141 (tpp) REVERT: i 32 MET cc_start: 0.8380 (tpp) cc_final: 0.7941 (tpp) outliers start: 156 outliers final: 94 residues processed: 441 average time/residue: 0.2212 time to fit residues: 155.1890 Evaluate side-chains 359 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 258 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 107 PHE Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 4 residue 73 LEU Chi-restraints excluded: chain 4 residue 92 VAL Chi-restraints excluded: chain 6 residue 513 VAL Chi-restraints excluded: chain 6 residue 534 SER Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 538 THR Chi-restraints excluded: chain 6 residue 583 VAL Chi-restraints excluded: chain 6 residue 598 CYS Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 635 ILE Chi-restraints excluded: chain 6 residue 639 THR Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 48 ILE Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 47 ILE Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain h residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 7 optimal weight: 5.9990 chunk 191 optimal weight: 0.1980 chunk 143 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 234 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 351 optimal weight: 0.9980 chunk 321 optimal weight: 9.9990 chunk 305 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS B 72 HIS B 156 ASN C 72 HIS ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.062638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.043761 restraints weight = 147392.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.045313 restraints weight = 71709.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.046312 restraints weight = 47254.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.046921 restraints weight = 36941.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.047246 restraints weight = 32020.536| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32997 Z= 0.125 Angle : 0.692 12.057 45120 Z= 0.334 Chirality : 0.045 0.369 5371 Planarity : 0.004 0.063 5463 Dihedral : 6.319 59.073 4196 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.13 % Allowed : 15.39 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.81 (0.13), residues: 3777 helix: 0.36 (0.26), residues: 399 sheet: -1.16 (0.14), residues: 1212 loop : -1.53 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 62 TYR 0.020 0.001 TYR Q 32 PHE 0.021 0.002 PHE f 115 TRP 0.014 0.001 TRP E 596 HIS 0.006 0.001 HIS X 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (32812) covalent geometry : angle 0.66361 / 0.33 (44619) SS BOND : bond 0.00302 / 0.20 ( 54) SS BOND : angle 0.88612 / 0.66 ( 108) hydrogen bonds : bond 0.03259 / 2.10 ( 1064) hydrogen bonds : angle 6.16627 / 4.29 ( 2817) link_ALPHA1-2 : bond 0.00525 / 0.26 ( 3) link_ALPHA1-2 : angle 1.47005 / 0.86 ( 9) link_ALPHA1-3 : bond 0.00671 / 0.43 ( 18) link_ALPHA1-3 : angle 1.57863 / 1.07 ( 54) link_ALPHA1-6 : bond 0.00390 / 0.22 ( 11) link_ALPHA1-6 : angle 1.46116 / 0.96 ( 33) link_BETA1-4 : bond 0.00434 / 0.29 ( 72) link_BETA1-4 : angle 2.09426 / 1.44 ( 216) link_NAG-ASN : bond 0.00489 / 0.31 ( 27) link_NAG-ASN : angle 2.91241 / 1.92 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 324 time to evaluate : 1.214 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: 1 94 ARG cc_start: 0.7781 (tmm160) cc_final: 0.7507 (ttp80) REVERT: 2 45 ARG cc_start: 0.9056 (tpm170) cc_final: 0.8663 (tpm170) REVERT: 3 64 LYS cc_start: 0.8430 (mtmm) cc_final: 0.8203 (ptpp) REVERT: 6 584 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8008 (tm-30) REVERT: 6 601 LYS cc_start: 0.8971 (mttt) cc_final: 0.8481 (ttpt) REVERT: 6 647 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8456 (mm-30) REVERT: 6 654 GLU cc_start: 0.8937 (tp30) cc_final: 0.8636 (tp30) REVERT: A 100 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8890 (ptp) REVERT: A 104 MET cc_start: 0.9440 (ttm) cc_final: 0.9139 (ttt) REVERT: A 373 THR cc_start: 0.9598 (t) cc_final: 0.9378 (t) REVERT: B 104 MET cc_start: 0.9448 (ttm) cc_final: 0.9114 (ttm) REVERT: B 475 MET cc_start: 0.8845 (mmm) cc_final: 0.8614 (mmm) REVERT: C 104 MET cc_start: 0.9514 (OUTLIER) cc_final: 0.8575 (ttm) REVERT: D 601 LYS cc_start: 0.8818 (mttt) cc_final: 0.8494 (ttmm) REVERT: D 659 ASP cc_start: 0.9073 (t0) cc_final: 0.8850 (m-30) REVERT: E 584 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8082 (tm-30) REVERT: E 601 LYS cc_start: 0.8850 (mttt) cc_final: 0.8579 (ttmm) REVERT: E 659 ASP cc_start: 0.9005 (t0) cc_final: 0.8803 (m-30) REVERT: H 64 LYS cc_start: 0.8472 (mtmm) cc_final: 0.8110 (ptpp) REVERT: H 94 ARG cc_start: 0.7843 (tmm160) cc_final: 0.7411 (ttp80) REVERT: N 20 ARG cc_start: 0.6975 (mtm-85) cc_final: 0.6377 (mtm-85) REVERT: N 54 ARG cc_start: 0.8595 (ptt-90) cc_final: 0.8252 (ptt90) REVERT: N 96 TRP cc_start: 0.8139 (m100) cc_final: 0.7414 (m100) REVERT: Q 3 GLN cc_start: 0.8238 (mp10) cc_final: 0.7679 (mp10) REVERT: Q 118 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8531 (tm-30) REVERT: X 30 ARG cc_start: 0.8757 (tpp80) cc_final: 0.8042 (tpp80) REVERT: X 44 GLN cc_start: 0.8294 (pp30) cc_final: 0.8062 (pp30) REVERT: X 53 ASP cc_start: 0.8219 (p0) cc_final: 0.7514 (p0) REVERT: X 64 LYS cc_start: 0.9119 (tppt) cc_final: 0.8827 (tppt) REVERT: X 100 MET cc_start: 0.8913 (mpp) cc_final: 0.8403 (mmm) REVERT: Y 30 ARG cc_start: 0.8766 (tpp80) cc_final: 0.8276 (tpp80) REVERT: Y 53 ASP cc_start: 0.8004 (p0) cc_final: 0.6921 (p0) REVERT: Y 64 LYS cc_start: 0.9059 (tppt) cc_final: 0.8535 (tppt) REVERT: Y 100 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8121 (mt-10) REVERT: Z 67 THR cc_start: 0.9504 (OUTLIER) cc_final: 0.9037 (p) REVERT: Z 96 TRP cc_start: 0.7890 (m100) cc_final: 0.7413 (m100) REVERT: a 20 ARG cc_start: 0.6692 (mtm-85) cc_final: 0.6457 (mtm-85) REVERT: a 96 TRP cc_start: 0.8024 (m100) cc_final: 0.7698 (m100) REVERT: f 70 MET cc_start: 0.8907 (mtm) cc_final: 0.8687 (mtm) REVERT: g 111 TYR cc_start: 0.8734 (m-80) cc_final: 0.8198 (m-80) REVERT: h 32 MET cc_start: 0.8446 (tpp) cc_final: 0.8031 (tpp) REVERT: i 32 MET cc_start: 0.8117 (tpp) cc_final: 0.7772 (tpp) outliers start: 104 outliers final: 70 residues processed: 409 average time/residue: 0.2234 time to fit residues: 144.5702 Evaluate side-chains 349 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 276 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 2 residue 92 VAL Chi-restraints excluded: chain 4 residue 73 LEU Chi-restraints excluded: chain 4 residue 92 VAL Chi-restraints excluded: chain 6 residue 513 VAL Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 632 ASP Chi-restraints excluded: chain 6 residue 635 ILE Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain f residue 37 VAL Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain i residue 40 ARG Chi-restraints excluded: chain i residue 77 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 120 optimal weight: 1.9990 chunk 329 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 296 optimal weight: 5.9990 chunk 205 optimal weight: 0.0470 chunk 288 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 203 optimal weight: 8.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 38 GLN ** 6 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN H 3 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.061665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.042658 restraints weight = 150508.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.044189 restraints weight = 74104.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.045167 restraints weight = 49206.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.045756 restraints weight = 38646.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.046125 restraints weight = 33665.022| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32997 Z= 0.199 Angle : 0.706 11.536 45120 Z= 0.340 Chirality : 0.044 0.345 5371 Planarity : 0.004 0.053 5463 Dihedral : 6.035 59.817 4188 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.82 % Allowed : 15.87 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.62 (0.13), residues: 3777 helix: 0.41 (0.26), residues: 417 sheet: -1.05 (0.14), residues: 1242 loop : -1.38 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 1 13 TYR 0.014 0.001 TYR Y 50 PHE 0.024 0.002 PHE f 115 TRP 0.015 0.001 TRP B 96 HIS 0.006 0.001 HIS X 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (32812) covalent geometry : angle 0.67549 / 0.33 (44619) SS BOND : bond 0.00343 / 0.20 ( 54) SS BOND : angle 0.94864 / 0.68 ( 108) hydrogen bonds : bond 0.03282 / 2.13 ( 1064) hydrogen bonds : angle 6.00484 / 4.18 ( 2817) link_ALPHA1-2 : bond 0.00381 / 0.19 ( 3) link_ALPHA1-2 : angle 1.48789 / 0.92 ( 9) link_ALPHA1-3 : bond 0.00618 / 0.40 ( 18) link_ALPHA1-3 : angle 1.66175 / 1.13 ( 54) link_ALPHA1-6 : bond 0.00309 / 0.18 ( 11) link_ALPHA1-6 : angle 1.48809 / 0.97 ( 33) link_BETA1-4 : bond 0.00391 / 0.27 ( 72) link_BETA1-4 : angle 2.16796 / 1.48 ( 216) link_NAG-ASN : bond 0.00585 / 0.36 ( 27) link_NAG-ASN : angle 3.05463 / 2.01 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 287 time to evaluate : 1.179 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: 1 94 ARG cc_start: 0.7703 (tmm160) cc_final: 0.7453 (ttp80) REVERT: 2 45 ARG cc_start: 0.9101 (tpm170) cc_final: 0.8685 (tpm170) REVERT: 6 584 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8570 (tm-30) REVERT: 6 601 LYS cc_start: 0.9011 (mttt) cc_final: 0.8587 (ttpp) REVERT: 6 603 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8264 (mm) REVERT: 6 647 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8487 (mm-30) REVERT: A 100 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.8920 (ptp) REVERT: A 373 THR cc_start: 0.9657 (t) cc_final: 0.9399 (t) REVERT: A 480 ARG cc_start: 0.9434 (OUTLIER) cc_final: 0.8380 (mtm110) REVERT: B 475 MET cc_start: 0.8854 (mmm) cc_final: 0.8626 (mmm) REVERT: C 100 MET cc_start: 0.9318 (OUTLIER) cc_final: 0.9030 (ptp) REVERT: C 104 MET cc_start: 0.9542 (OUTLIER) cc_final: 0.8680 (ttm) REVERT: D 601 LYS cc_start: 0.8870 (mttt) cc_final: 0.8560 (ttmm) REVERT: D 659 ASP cc_start: 0.9075 (t0) cc_final: 0.8863 (m-30) REVERT: E 584 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8048 (tm-30) REVERT: E 601 LYS cc_start: 0.8913 (mttt) cc_final: 0.8610 (ttmm) REVERT: E 659 ASP cc_start: 0.9033 (t0) cc_final: 0.8814 (m-30) REVERT: H 94 ARG cc_start: 0.7795 (tmm160) cc_final: 0.7364 (ttp80) REVERT: L 42 GLN cc_start: 0.6428 (OUTLIER) cc_final: 0.6145 (pt0) REVERT: N 54 ARG cc_start: 0.8622 (ptt-90) cc_final: 0.8244 (ptt90) REVERT: N 67 THR cc_start: 0.9486 (OUTLIER) cc_final: 0.8998 (p) REVERT: N 96 TRP cc_start: 0.8218 (m100) cc_final: 0.7461 (m100) REVERT: Q 3 GLN cc_start: 0.8289 (mp10) cc_final: 0.7677 (mp10) REVERT: Q 118 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8691 (tm-30) REVERT: X 30 ARG cc_start: 0.8824 (tpp80) cc_final: 0.8133 (tpp80) REVERT: X 44 GLN cc_start: 0.8292 (pp30) cc_final: 0.8080 (pp30) REVERT: X 53 ASP cc_start: 0.8385 (p0) cc_final: 0.7849 (p0) REVERT: X 64 LYS cc_start: 0.9072 (tppt) cc_final: 0.8855 (tppt) REVERT: Y 30 ARG cc_start: 0.8843 (tpp80) cc_final: 0.8325 (tpp80) REVERT: Y 53 ASP cc_start: 0.8169 (p0) cc_final: 0.7154 (p0) REVERT: Y 64 LYS cc_start: 0.9076 (tppt) cc_final: 0.8665 (tppt) REVERT: Y 100 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8224 (mt-10) REVERT: Z 67 THR cc_start: 0.9487 (OUTLIER) cc_final: 0.9005 (p) REVERT: Z 96 TRP cc_start: 0.7984 (m100) cc_final: 0.7446 (m100) REVERT: a 20 ARG cc_start: 0.6749 (mtm-85) cc_final: 0.6522 (mtm-85) REVERT: a 67 THR cc_start: 0.9440 (OUTLIER) cc_final: 0.8904 (p) REVERT: g 111 TYR cc_start: 0.8727 (m-80) cc_final: 0.8319 (m-80) REVERT: h 32 MET cc_start: 0.8304 (tpp) cc_final: 0.7739 (tpp) REVERT: i 32 MET cc_start: 0.8224 (tpp) cc_final: 0.7876 (tpp) outliers start: 127 outliers final: 87 residues processed: 395 average time/residue: 0.2112 time to fit residues: 133.3843 Evaluate side-chains 367 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 271 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 4 residue 73 LEU Chi-restraints excluded: chain 4 residue 92 VAL Chi-restraints excluded: chain 6 residue 513 VAL Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 583 VAL Chi-restraints excluded: chain 6 residue 603 ILE Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 635 ILE Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 480 ARG Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 647 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain f residue 37 VAL Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain i residue 40 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 250 optimal weight: 0.9980 chunk 31 optimal weight: 20.0000 chunk 247 optimal weight: 9.9990 chunk 339 optimal weight: 7.9990 chunk 333 optimal weight: 0.7980 chunk 245 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 70 optimal weight: 0.0020 chunk 101 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.062186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.043188 restraints weight = 149336.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.044742 restraints weight = 73268.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.045724 restraints weight = 48559.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.046321 restraints weight = 38176.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.046677 restraints weight = 33218.881| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32997 Z= 0.154 Angle : 0.680 11.025 45120 Z= 0.328 Chirality : 0.044 0.349 5371 Planarity : 0.004 0.051 5463 Dihedral : 5.872 55.399 4188 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.37 % Allowed : 16.62 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.47 (0.14), residues: 3777 helix: 0.49 (0.26), residues: 414 sheet: -1.00 (0.14), residues: 1254 loop : -1.23 (0.14), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 13 TYR 0.024 0.001 TYR B 318 PHE 0.022 0.002 PHE f 115 TRP 0.014 0.001 TRP D 571 HIS 0.005 0.001 HIS X 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (32812) covalent geometry : angle 0.65211 / 0.32 (44619) SS BOND : bond 0.00284 / 0.16 ( 54) SS BOND : angle 0.96180 / 0.69 ( 108) hydrogen bonds : bond 0.03102 / 2.01 ( 1064) hydrogen bonds : angle 5.82979 / 4.06 ( 2817) link_ALPHA1-2 : bond 0.00449 / 0.22 ( 3) link_ALPHA1-2 : angle 1.43855 / 0.87 ( 9) link_ALPHA1-3 : bond 0.00617 / 0.40 ( 18) link_ALPHA1-3 : angle 1.58257 / 1.08 ( 54) link_ALPHA1-6 : bond 0.00341 / 0.19 ( 11) link_ALPHA1-6 : angle 1.46406 / 0.96 ( 33) link_BETA1-4 : bond 0.00397 / 0.27 ( 72) link_BETA1-4 : angle 2.06046 / 1.40 ( 216) link_NAG-ASN : bond 0.00485 / 0.31 ( 27) link_NAG-ASN : angle 2.87027 / 1.89 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 302 time to evaluate : 1.245 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: 1 94 ARG cc_start: 0.7652 (tmm160) cc_final: 0.7450 (ttp80) REVERT: 3 13 ARG cc_start: 0.8932 (tpp80) cc_final: 0.8730 (tpp-160) REVERT: 6 584 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8571 (tm-30) REVERT: 6 601 LYS cc_start: 0.8998 (mttt) cc_final: 0.8522 (ttpp) REVERT: 6 603 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8247 (mm) REVERT: 6 647 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8441 (mm-30) REVERT: A 100 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8883 (ptp) REVERT: A 373 THR cc_start: 0.9606 (t) cc_final: 0.9325 (t) REVERT: A 480 ARG cc_start: 0.9409 (OUTLIER) cc_final: 0.8352 (mtm110) REVERT: B 475 MET cc_start: 0.8826 (mmm) cc_final: 0.8603 (mmm) REVERT: C 104 MET cc_start: 0.9519 (OUTLIER) cc_final: 0.8571 (ttm) REVERT: D 601 LYS cc_start: 0.8846 (mttt) cc_final: 0.8516 (ttmm) REVERT: E 584 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7995 (tm-30) REVERT: E 601 LYS cc_start: 0.8897 (mttt) cc_final: 0.8594 (ttmm) REVERT: E 659 ASP cc_start: 0.8996 (t0) cc_final: 0.8783 (m-30) REVERT: H 64 LYS cc_start: 0.8516 (mtmm) cc_final: 0.8192 (ptpp) REVERT: H 94 ARG cc_start: 0.7669 (tmm160) cc_final: 0.7299 (ttp80) REVERT: N 54 ARG cc_start: 0.8627 (ptt-90) cc_final: 0.8243 (ptt90) REVERT: N 67 THR cc_start: 0.9488 (OUTLIER) cc_final: 0.9004 (p) REVERT: N 96 TRP cc_start: 0.8181 (m100) cc_final: 0.7402 (m100) REVERT: Q 3 GLN cc_start: 0.8336 (mp10) cc_final: 0.7725 (mp10) REVERT: Q 118 GLN cc_start: 0.9033 (tm-30) cc_final: 0.8674 (tm-30) REVERT: R 32 MET cc_start: 0.8745 (tpp) cc_final: 0.7921 (tpp) REVERT: X 30 ARG cc_start: 0.8866 (tpp80) cc_final: 0.8171 (tpp80) REVERT: X 44 GLN cc_start: 0.8254 (pp30) cc_final: 0.8054 (pp30) REVERT: X 53 ASP cc_start: 0.8416 (p0) cc_final: 0.7764 (p0) REVERT: X 100 LYS cc_start: 0.9453 (OUTLIER) cc_final: 0.9193 (mttm) REVERT: X 100 MET cc_start: 0.8870 (mpp) cc_final: 0.8418 (mmm) REVERT: Y 30 ARG cc_start: 0.8848 (tpp80) cc_final: 0.8392 (tpp80) REVERT: Y 64 LYS cc_start: 0.9004 (tppt) cc_final: 0.8575 (tppt) REVERT: Y 100 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8152 (mt-10) REVERT: Z 67 THR cc_start: 0.9500 (OUTLIER) cc_final: 0.9025 (p) REVERT: a 20 ARG cc_start: 0.6751 (mtm-85) cc_final: 0.6529 (mtm-85) REVERT: a 67 THR cc_start: 0.9466 (OUTLIER) cc_final: 0.8942 (p) REVERT: a 96 TRP cc_start: 0.8167 (m100) cc_final: 0.7688 (m100) REVERT: f 3 GLN cc_start: 0.8265 (mp10) cc_final: 0.8044 (mp10) REVERT: g 111 TYR cc_start: 0.8705 (m-80) cc_final: 0.8325 (m-80) REVERT: h 32 MET cc_start: 0.8301 (tpp) cc_final: 0.7670 (tpp) REVERT: i 32 MET cc_start: 0.8081 (tpp) cc_final: 0.7687 (tpp) REVERT: i 36 TYR cc_start: 0.9272 (m-80) cc_final: 0.8835 (m-80) outliers start: 112 outliers final: 81 residues processed: 399 average time/residue: 0.2142 time to fit residues: 137.0181 Evaluate side-chains 370 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 281 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 4 residue 73 LEU Chi-restraints excluded: chain 6 residue 513 VAL Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 538 THR Chi-restraints excluded: chain 6 residue 603 ILE Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 635 ILE Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 480 ARG Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 647 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 100 LYS Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain f residue 37 VAL Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain i residue 40 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 193 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 330 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 253 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 208 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 38 GLN ** 2 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.060274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.041150 restraints weight = 153003.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.042634 restraints weight = 76908.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.043572 restraints weight = 51838.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.044140 restraints weight = 41207.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.044469 restraints weight = 36067.788| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 32997 Z= 0.316 Angle : 0.792 10.562 45120 Z= 0.380 Chirality : 0.046 0.334 5371 Planarity : 0.004 0.052 5463 Dihedral : 6.113 58.145 4188 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.94 % Allowed : 17.16 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.53 (0.14), residues: 3777 helix: 0.66 (0.27), residues: 396 sheet: -1.02 (0.15), residues: 1236 loop : -1.32 (0.14), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 1 13 TYR 0.016 0.002 TYR 4 87 PHE 0.027 0.003 PHE g 115 TRP 0.021 0.002 TRP D 571 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.32 (32812) covalent geometry : angle 0.76134 / 0.37 (44619) SS BOND : bond 0.00620 / 0.42 ( 54) SS BOND : angle 1.24454 / 0.89 ( 108) hydrogen bonds : bond 0.03505 / 2.28 ( 1064) hydrogen bonds : angle 6.02668 / 4.18 ( 2817) link_ALPHA1-2 : bond 0.00292 / 0.15 ( 3) link_ALPHA1-2 : angle 1.59226 / 1.01 ( 9) link_ALPHA1-3 : bond 0.00562 / 0.37 ( 18) link_ALPHA1-3 : angle 1.86905 / 1.26 ( 54) link_ALPHA1-6 : bond 0.00258 / 0.14 ( 11) link_ALPHA1-6 : angle 1.57691 / 1.02 ( 33) link_BETA1-4 : bond 0.00431 / 0.29 ( 72) link_BETA1-4 : angle 2.29030 / 1.55 ( 216) link_NAG-ASN : bond 0.00899 / 0.54 ( 27) link_NAG-ASN : angle 3.26553 / 2.15 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 278 time to evaluate : 1.262 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: 1 94 ARG cc_start: 0.7769 (tmm160) cc_final: 0.7505 (ttp80) REVERT: 4 45 ARG cc_start: 0.8276 (ttm170) cc_final: 0.7863 (ttp-170) REVERT: 6 584 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8535 (tm-30) REVERT: 6 601 LYS cc_start: 0.9043 (mttt) cc_final: 0.8748 (ttmm) REVERT: A 114 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8153 (tm-30) REVERT: A 373 THR cc_start: 0.9681 (t) cc_final: 0.9440 (t) REVERT: A 480 ARG cc_start: 0.9497 (OUTLIER) cc_final: 0.8443 (mtm110) REVERT: C 104 MET cc_start: 0.9542 (OUTLIER) cc_final: 0.8719 (ttm) REVERT: D 545 LEU cc_start: 0.9313 (mt) cc_final: 0.9031 (mm) REVERT: D 601 LYS cc_start: 0.8939 (mttt) cc_final: 0.8669 (ttmm) REVERT: E 571 TRP cc_start: 0.7947 (m-90) cc_final: 0.7686 (m-90) REVERT: E 584 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7988 (tm-30) REVERT: E 601 LYS cc_start: 0.8963 (mttt) cc_final: 0.8697 (ttmm) REVERT: E 659 ASP cc_start: 0.9013 (t0) cc_final: 0.8769 (m-30) REVERT: H 94 ARG cc_start: 0.7788 (tmm160) cc_final: 0.7293 (ttp80) REVERT: M 13 LYS cc_start: 0.9143 (ttpp) cc_final: 0.8934 (ttpp) REVERT: N 54 ARG cc_start: 0.8630 (ptt-90) cc_final: 0.8242 (ptm-80) REVERT: N 67 THR cc_start: 0.9451 (OUTLIER) cc_final: 0.8926 (p) REVERT: Q 3 GLN cc_start: 0.8382 (mp10) cc_final: 0.7814 (mp10) REVERT: Q 118 GLN cc_start: 0.9133 (tm-30) cc_final: 0.8706 (tm-30) REVERT: R 32 MET cc_start: 0.8937 (tpp) cc_final: 0.8097 (tpp) REVERT: X 30 ARG cc_start: 0.8895 (tpp80) cc_final: 0.8257 (tpp80) REVERT: X 38 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.7683 (tmm-80) REVERT: X 53 ASP cc_start: 0.8596 (p0) cc_final: 0.8033 (p0) REVERT: X 100 MET cc_start: 0.8992 (mpp) cc_final: 0.8588 (mmm) REVERT: Y 30 ARG cc_start: 0.8940 (tpp80) cc_final: 0.8501 (tpp80) REVERT: Y 38 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8725 (tmm-80) REVERT: Y 64 LYS cc_start: 0.9102 (tppt) cc_final: 0.8696 (tppt) REVERT: Y 100 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8182 (mt-10) REVERT: Z 67 THR cc_start: 0.9469 (OUTLIER) cc_final: 0.8954 (p) REVERT: Z 96 TRP cc_start: 0.8148 (m100) cc_final: 0.7491 (m100) REVERT: a 20 ARG cc_start: 0.6864 (mtm-85) cc_final: 0.6661 (mtm-85) REVERT: a 67 THR cc_start: 0.9419 (OUTLIER) cc_final: 0.9005 (p) REVERT: f 70 MET cc_start: 0.8759 (mtm) cc_final: 0.8522 (mtm) REVERT: g 111 TYR cc_start: 0.8797 (m-80) cc_final: 0.8472 (m-80) REVERT: h 32 MET cc_start: 0.8585 (tpp) cc_final: 0.7945 (tpp) REVERT: h 77 LYS cc_start: 0.9386 (mttt) cc_final: 0.9177 (ptpt) REVERT: i 32 MET cc_start: 0.8366 (tpp) cc_final: 0.8114 (tpp) outliers start: 131 outliers final: 92 residues processed: 394 average time/residue: 0.2026 time to fit residues: 127.8083 Evaluate side-chains 361 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 261 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 4 residue 73 LEU Chi-restraints excluded: chain 4 residue 92 VAL Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 538 THR Chi-restraints excluded: chain 6 residue 583 VAL Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 635 ILE Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 480 ARG Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 647 GLU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 38 ARG Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 38 ARG Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Y residue 89 ILE Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 47 ILE Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain i residue 40 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 215 optimal weight: 3.9990 chunk 321 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 289 optimal weight: 5.9990 chunk 329 optimal weight: 1.9990 chunk 310 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.060913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.041825 restraints weight = 150734.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.043369 restraints weight = 73317.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.044346 restraints weight = 48370.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.044941 restraints weight = 37876.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.045315 restraints weight = 32852.627| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32997 Z= 0.195 Angle : 0.723 18.033 45120 Z= 0.348 Chirality : 0.045 0.347 5371 Planarity : 0.004 0.049 5463 Dihedral : 5.919 52.597 4186 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.43 % Allowed : 18.24 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.39 (0.14), residues: 3777 helix: 0.81 (0.27), residues: 396 sheet: -0.95 (0.15), residues: 1230 loop : -1.22 (0.14), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 13 TYR 0.018 0.001 TYR 2 87 PHE 0.024 0.002 PHE g 115 TRP 0.017 0.001 TRP D 571 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (32812) covalent geometry : angle 0.69608 / 0.34 (44619) SS BOND : bond 0.00352 / 0.21 ( 54) SS BOND : angle 1.07782 / 0.75 ( 108) hydrogen bonds : bond 0.03206 / 2.08 ( 1064) hydrogen bonds : angle 5.88077 / 4.09 ( 2817) link_ALPHA1-2 : bond 0.00402 / 0.20 ( 3) link_ALPHA1-2 : angle 1.43999 / 0.87 ( 9) link_ALPHA1-3 : bond 0.00594 / 0.38 ( 18) link_ALPHA1-3 : angle 1.70739 / 1.16 ( 54) link_ALPHA1-6 : bond 0.00319 / 0.18 ( 11) link_ALPHA1-6 : angle 1.49066 / 0.97 ( 33) link_BETA1-4 : bond 0.00380 / 0.26 ( 72) link_BETA1-4 : angle 2.09783 / 1.43 ( 216) link_NAG-ASN : bond 0.00559 / 0.35 ( 27) link_NAG-ASN : angle 2.87688 / 1.91 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 288 time to evaluate : 1.279 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: 1 94 ARG cc_start: 0.7647 (tmm160) cc_final: 0.7415 (ttp80) REVERT: 4 45 ARG cc_start: 0.8365 (ttm170) cc_final: 0.7943 (ttp-170) REVERT: 6 584 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8580 (tm-30) REVERT: 6 601 LYS cc_start: 0.9016 (mttt) cc_final: 0.8647 (ttmm) REVERT: A 114 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: A 373 THR cc_start: 0.9633 (t) cc_final: 0.9360 (t) REVERT: A 480 ARG cc_start: 0.9398 (OUTLIER) cc_final: 0.8342 (mtm110) REVERT: C 104 MET cc_start: 0.9570 (OUTLIER) cc_final: 0.8740 (ttm) REVERT: D 601 LYS cc_start: 0.8923 (mttt) cc_final: 0.8549 (ttmm) REVERT: E 601 LYS cc_start: 0.8925 (mttt) cc_final: 0.8624 (ttmm) REVERT: E 659 ASP cc_start: 0.9011 (t0) cc_final: 0.8803 (m-30) REVERT: H 94 ARG cc_start: 0.7620 (tmm160) cc_final: 0.7240 (ttp80) REVERT: M 13 LYS cc_start: 0.9216 (ttpp) cc_final: 0.8962 (ttpp) REVERT: N 54 ARG cc_start: 0.8647 (ptt-90) cc_final: 0.8234 (ptm-80) REVERT: N 67 THR cc_start: 0.9470 (OUTLIER) cc_final: 0.8964 (p) REVERT: N 96 TRP cc_start: 0.8264 (m100) cc_final: 0.7604 (m100) REVERT: Q 3 GLN cc_start: 0.8393 (mp10) cc_final: 0.7796 (mp10) REVERT: Q 118 GLN cc_start: 0.9085 (tm-30) cc_final: 0.8642 (tm-30) REVERT: X 30 ARG cc_start: 0.8880 (tpp80) cc_final: 0.8187 (tpp80) REVERT: X 38 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.7672 (tmm-80) REVERT: X 53 ASP cc_start: 0.8577 (p0) cc_final: 0.7938 (p0) REVERT: X 100 MET cc_start: 0.9018 (mpp) cc_final: 0.8774 (mmm) REVERT: Y 30 ARG cc_start: 0.8900 (tpp80) cc_final: 0.8366 (tpp80) REVERT: Y 53 ASP cc_start: 0.8343 (p0) cc_final: 0.6900 (p0) REVERT: Y 64 LYS cc_start: 0.9062 (tppt) cc_final: 0.8658 (tppt) REVERT: Y 100 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8180 (mt-10) REVERT: Z 67 THR cc_start: 0.9484 (OUTLIER) cc_final: 0.8976 (p) REVERT: a 20 ARG cc_start: 0.6823 (mtm-85) cc_final: 0.6621 (mtm-85) REVERT: a 67 THR cc_start: 0.9421 (OUTLIER) cc_final: 0.9018 (p) REVERT: a 96 TRP cc_start: 0.8277 (m100) cc_final: 0.7803 (m100) REVERT: f 70 MET cc_start: 0.8830 (mtm) cc_final: 0.8564 (mtm) REVERT: g 111 TYR cc_start: 0.8785 (m-80) cc_final: 0.8466 (m-80) REVERT: h 32 MET cc_start: 0.8491 (tpp) cc_final: 0.7828 (tpp) REVERT: h 77 LYS cc_start: 0.9362 (mttt) cc_final: 0.9142 (ptpt) outliers start: 114 outliers final: 87 residues processed: 389 average time/residue: 0.2056 time to fit residues: 128.6365 Evaluate side-chains 368 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 274 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 4 residue 73 LEU Chi-restraints excluded: chain 6 residue 513 VAL Chi-restraints excluded: chain 6 residue 518 VAL Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 538 THR Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 639 THR Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 480 ARG Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 38 ARG Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Y residue 89 ILE Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain f residue 37 VAL Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain i residue 40 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 299 optimal weight: 10.0000 chunk 345 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 315 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 271 optimal weight: 0.9990 chunk 371 optimal weight: 10.0000 chunk 209 optimal weight: 0.9990 chunk 300 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 ASN ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.060962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.042003 restraints weight = 149613.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.043505 restraints weight = 74426.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.044454 restraints weight = 49678.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.045029 restraints weight = 39208.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.045387 restraints weight = 34187.432| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32997 Z= 0.196 Angle : 0.723 16.731 45120 Z= 0.347 Chirality : 0.044 0.344 5371 Planarity : 0.004 0.053 5463 Dihedral : 5.793 51.743 4184 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.31 % Allowed : 18.58 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.35 (0.14), residues: 3777 helix: 0.83 (0.26), residues: 399 sheet: -0.91 (0.15), residues: 1248 loop : -1.20 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 4 77 TYR 0.017 0.001 TYR 2 87 PHE 0.024 0.002 PHE g 115 TRP 0.026 0.002 TRP D 571 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (32812) covalent geometry : angle 0.69612 / 0.34 (44619) SS BOND : bond 0.00382 / 0.22 ( 54) SS BOND : angle 1.07403 / 0.73 ( 108) hydrogen bonds : bond 0.03184 / 2.06 ( 1064) hydrogen bonds : angle 5.82462 / 4.05 ( 2817) link_ALPHA1-2 : bond 0.00368 / 0.18 ( 3) link_ALPHA1-2 : angle 1.46569 / 0.90 ( 9) link_ALPHA1-3 : bond 0.00581 / 0.37 ( 18) link_ALPHA1-3 : angle 1.66985 / 1.13 ( 54) link_ALPHA1-6 : bond 0.00322 / 0.18 ( 11) link_ALPHA1-6 : angle 1.48504 / 0.97 ( 33) link_BETA1-4 : bond 0.00385 / 0.26 ( 72) link_BETA1-4 : angle 2.08717 / 1.42 ( 216) link_NAG-ASN : bond 0.00565 / 0.35 ( 27) link_NAG-ASN : angle 2.88657 / 1.91 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 289 time to evaluate : 1.258 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: 1 94 ARG cc_start: 0.7623 (tmm160) cc_final: 0.7411 (ttp80) REVERT: 4 45 ARG cc_start: 0.8332 (ttm170) cc_final: 0.7887 (ttp-170) REVERT: 6 584 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8602 (tm-30) REVERT: 6 601 LYS cc_start: 0.8990 (mttt) cc_final: 0.8589 (ttmm) REVERT: A 373 THR cc_start: 0.9614 (t) cc_final: 0.9338 (t) REVERT: A 480 ARG cc_start: 0.9386 (OUTLIER) cc_final: 0.8321 (mtm110) REVERT: C 104 MET cc_start: 0.9572 (OUTLIER) cc_final: 0.8730 (ttm) REVERT: D 601 LYS cc_start: 0.8908 (mttt) cc_final: 0.8527 (ttmm) REVERT: E 584 GLU cc_start: 0.8567 (tm-30) cc_final: 0.7794 (tm-30) REVERT: E 601 LYS cc_start: 0.8936 (mttt) cc_final: 0.8634 (ttmm) REVERT: H 64 LYS cc_start: 0.8541 (mtmm) cc_final: 0.8187 (ptpp) REVERT: H 94 ARG cc_start: 0.7573 (tmm160) cc_final: 0.7219 (ttp80) REVERT: M 13 LYS cc_start: 0.9188 (ttpp) cc_final: 0.8918 (ttpp) REVERT: M 100 GLU cc_start: 0.8639 (mt-10) cc_final: 0.7992 (tt0) REVERT: N 54 ARG cc_start: 0.8593 (ptt-90) cc_final: 0.8197 (ptt90) REVERT: N 67 THR cc_start: 0.9461 (OUTLIER) cc_final: 0.8951 (p) REVERT: N 96 TRP cc_start: 0.8322 (m100) cc_final: 0.7578 (m100) REVERT: Q 3 GLN cc_start: 0.8390 (mp10) cc_final: 0.7778 (mp10) REVERT: Q 118 GLN cc_start: 0.9123 (tm-30) cc_final: 0.8668 (tm-30) REVERT: X 30 ARG cc_start: 0.8930 (tpp80) cc_final: 0.8289 (tpp80) REVERT: X 38 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.7602 (tmm-80) REVERT: X 53 ASP cc_start: 0.8639 (p0) cc_final: 0.7948 (p0) REVERT: X 100 MET cc_start: 0.9023 (mpp) cc_final: 0.8800 (mmm) REVERT: Y 30 ARG cc_start: 0.8943 (tpp80) cc_final: 0.8431 (tpp80) REVERT: Y 38 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8803 (tmm-80) REVERT: Y 53 ASP cc_start: 0.8419 (p0) cc_final: 0.7133 (p0) REVERT: Y 64 LYS cc_start: 0.9013 (tppt) cc_final: 0.8808 (tppt) REVERT: Y 100 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8183 (mt-10) REVERT: Z 67 THR cc_start: 0.9483 (OUTLIER) cc_final: 0.8980 (p) REVERT: Z 100 GLU cc_start: 0.8744 (pm20) cc_final: 0.8226 (pm20) REVERT: a 20 ARG cc_start: 0.6827 (mtm-85) cc_final: 0.6621 (mtm-85) REVERT: a 67 THR cc_start: 0.9421 (OUTLIER) cc_final: 0.9019 (p) REVERT: a 96 TRP cc_start: 0.8293 (m100) cc_final: 0.7820 (m100) REVERT: f 70 MET cc_start: 0.8840 (mtm) cc_final: 0.8578 (mtm) REVERT: g 3 GLN cc_start: 0.8336 (mp10) cc_final: 0.8078 (mp10) REVERT: h 32 MET cc_start: 0.8440 (tpp) cc_final: 0.7800 (tpp) REVERT: h 77 LYS cc_start: 0.9354 (mttt) cc_final: 0.9132 (ptpt) REVERT: i 36 TYR cc_start: 0.9284 (m-80) cc_final: 0.9054 (m-80) outliers start: 110 outliers final: 83 residues processed: 385 average time/residue: 0.2077 time to fit residues: 127.3862 Evaluate side-chains 362 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 272 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 4 residue 73 LEU Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 639 THR Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 480 ARG Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 38 ARG Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 38 ARG Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Y residue 89 ILE Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain f residue 37 VAL Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain i residue 40 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 161 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 308 optimal weight: 1.9990 chunk 300 optimal weight: 20.0000 chunk 168 optimal weight: 0.5980 chunk 121 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 227 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 39 GLN ** 2 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 GLN ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.061815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.042851 restraints weight = 149857.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.044381 restraints weight = 73139.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.045354 restraints weight = 48432.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.045953 restraints weight = 38057.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.046324 restraints weight = 33045.107| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32997 Z= 0.142 Angle : 0.710 16.888 45120 Z= 0.342 Chirality : 0.044 0.350 5371 Planarity : 0.004 0.051 5463 Dihedral : 5.625 54.202 4184 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.68 % Allowed : 19.30 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.27 (0.14), residues: 3777 helix: 0.54 (0.26), residues: 414 sheet: -0.83 (0.15), residues: 1233 loop : -1.10 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 588 TYR 0.017 0.001 TYR Z 49 PHE 0.020 0.002 PHE g 115 TRP 0.026 0.001 TRP D 571 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (32812) covalent geometry : angle 0.68609 / 0.34 (44619) SS BOND : bond 0.00289 / 0.16 ( 54) SS BOND : angle 0.93028 / 0.64 ( 108) hydrogen bonds : bond 0.03050 / 1.97 ( 1064) hydrogen bonds : angle 5.68672 / 3.96 ( 2817) link_ALPHA1-2 : bond 0.00443 / 0.22 ( 3) link_ALPHA1-2 : angle 1.43771 / 0.86 ( 9) link_ALPHA1-3 : bond 0.00611 / 0.39 ( 18) link_ALPHA1-3 : angle 1.56311 / 1.06 ( 54) link_ALPHA1-6 : bond 0.00370 / 0.21 ( 11) link_ALPHA1-6 : angle 1.45236 / 0.96 ( 33) link_BETA1-4 : bond 0.00401 / 0.27 ( 72) link_BETA1-4 : angle 1.99868 / 1.36 ( 216) link_NAG-ASN : bond 0.00472 / 0.30 ( 27) link_NAG-ASN : angle 2.71554 / 1.80 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 303 time to evaluate : 1.191 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: 4 45 ARG cc_start: 0.8397 (ttm170) cc_final: 0.7970 (ttp-170) REVERT: 6 584 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8613 (tm-30) REVERT: 6 601 LYS cc_start: 0.8898 (mttt) cc_final: 0.8477 (ttmm) REVERT: A 373 THR cc_start: 0.9597 (t) cc_final: 0.9312 (t) REVERT: B 125 LEU cc_start: 0.9665 (tp) cc_final: 0.9378 (tp) REVERT: B 173 TYR cc_start: 0.9146 (p90) cc_final: 0.8907 (p90) REVERT: C 104 MET cc_start: 0.9529 (OUTLIER) cc_final: 0.8586 (ttm) REVERT: D 601 LYS cc_start: 0.8855 (mttt) cc_final: 0.8487 (ttmm) REVERT: E 601 LYS cc_start: 0.8855 (mttt) cc_final: 0.8555 (ttmm) REVERT: H 64 LYS cc_start: 0.8537 (mtmm) cc_final: 0.8197 (ptpp) REVERT: H 94 ARG cc_start: 0.7489 (tmm160) cc_final: 0.7229 (ttp80) REVERT: M 13 LYS cc_start: 0.9209 (ttpp) cc_final: 0.8785 (ttpp) REVERT: M 16 GLU cc_start: 0.7387 (pt0) cc_final: 0.6570 (pt0) REVERT: M 100 GLU cc_start: 0.8594 (mt-10) cc_final: 0.7968 (tt0) REVERT: N 25 GLU cc_start: 0.7940 (tp30) cc_final: 0.7394 (pp20) REVERT: N 54 ARG cc_start: 0.8641 (ptt-90) cc_final: 0.8245 (ptt90) REVERT: N 67 THR cc_start: 0.9495 (OUTLIER) cc_final: 0.8984 (p) REVERT: N 96 TRP cc_start: 0.8234 (m100) cc_final: 0.7546 (m100) REVERT: Q 3 GLN cc_start: 0.8407 (mp10) cc_final: 0.7818 (mp10) REVERT: Q 118 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8668 (tm-30) REVERT: X 30 ARG cc_start: 0.8914 (tpp80) cc_final: 0.8286 (tpp80) REVERT: X 53 ASP cc_start: 0.8622 (p0) cc_final: 0.7850 (p0) REVERT: Y 30 ARG cc_start: 0.8894 (tpp80) cc_final: 0.8365 (tpp80) REVERT: Y 38 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8824 (tmm-80) REVERT: Y 53 ASP cc_start: 0.8411 (p0) cc_final: 0.7064 (p0) REVERT: Y 100 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8131 (mt-10) REVERT: Z 25 GLU cc_start: 0.7845 (tp30) cc_final: 0.7512 (pp20) REVERT: Z 67 THR cc_start: 0.9502 (OUTLIER) cc_final: 0.9051 (p) REVERT: a 20 ARG cc_start: 0.6885 (mtm-85) cc_final: 0.6672 (mtm-85) REVERT: a 67 THR cc_start: 0.9450 (OUTLIER) cc_final: 0.8901 (p) REVERT: a 96 TRP cc_start: 0.8204 (m100) cc_final: 0.7777 (m100) REVERT: a 100 GLU cc_start: 0.8857 (pm20) cc_final: 0.8656 (pm20) REVERT: f 70 MET cc_start: 0.8780 (mtm) cc_final: 0.8513 (mtm) REVERT: f 110 ASP cc_start: 0.8553 (p0) cc_final: 0.8295 (p0) REVERT: g 3 GLN cc_start: 0.8321 (mp10) cc_final: 0.8075 (mp10) REVERT: h 32 MET cc_start: 0.8298 (tpp) cc_final: 0.7645 (tpp) REVERT: i 36 TYR cc_start: 0.9287 (m-80) cc_final: 0.9017 (m-80) outliers start: 89 outliers final: 80 residues processed: 376 average time/residue: 0.2139 time to fit residues: 128.5053 Evaluate side-chains 369 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 284 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 4 residue 73 LEU Chi-restraints excluded: chain 6 residue 518 VAL Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 639 THR Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 38 ARG Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain f residue 31 ASP Chi-restraints excluded: chain f residue 37 VAL Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain i residue 40 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 178 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 359 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 332 optimal weight: 0.0570 chunk 66 optimal weight: 0.5980 chunk 256 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 205 optimal weight: 0.0270 chunk 157 optimal weight: 0.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN M 5 GLN M 23 ASN M 68 HIS X 68 HIS ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.062925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.044011 restraints weight = 147849.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.045589 restraints weight = 71054.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.046599 restraints weight = 46513.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.047216 restraints weight = 36205.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.047581 restraints weight = 31296.657| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32997 Z= 0.115 Angle : 0.696 16.950 45120 Z= 0.334 Chirality : 0.044 0.351 5371 Planarity : 0.004 0.054 5463 Dihedral : 5.368 56.242 4183 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.34 % Allowed : 19.84 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.08 (0.14), residues: 3777 helix: 0.92 (0.27), residues: 396 sheet: -0.68 (0.15), residues: 1230 loop : -1.02 (0.14), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 1 94 TYR 0.019 0.001 TYR N 49 PHE 0.018 0.001 PHE g 115 TRP 0.028 0.001 TRP D 571 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (32812) covalent geometry : angle 0.67359 / 0.33 (44619) SS BOND : bond 0.00206 / 0.12 ( 54) SS BOND : angle 0.87585 / 0.60 ( 108) hydrogen bonds : bond 0.02956 / 1.92 ( 1064) hydrogen bonds : angle 5.48480 / 3.82 ( 2817) link_ALPHA1-2 : bond 0.00472 / 0.24 ( 3) link_ALPHA1-2 : angle 1.45620 / 0.87 ( 9) link_ALPHA1-3 : bond 0.00652 / 0.42 ( 18) link_ALPHA1-3 : angle 1.46461 / 0.99 ( 54) link_ALPHA1-6 : bond 0.00424 / 0.24 ( 11) link_ALPHA1-6 : angle 1.42389 / 0.95 ( 33) link_BETA1-4 : bond 0.00463 / 0.32 ( 72) link_BETA1-4 : angle 1.91226 / 1.31 ( 216) link_NAG-ASN : bond 0.00480 / 0.30 ( 27) link_NAG-ASN : angle 2.60117 / 1.73 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5696.51 seconds wall clock time: 99 minutes 45.35 seconds (5985.35 seconds total)