Starting phenix.real_space_refine on Fri Mar 22 01:54:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6et5_3951/03_2024/6et5_3951_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6et5_3951/03_2024/6et5_3951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6et5_3951/03_2024/6et5_3951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6et5_3951/03_2024/6et5_3951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6et5_3951/03_2024/6et5_3951_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6et5_3951/03_2024/6et5_3951_updated.pdb" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.004 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: 6 Type Number sf(0) Gaussians Fe 5 7.16 5 Mg 38 5.21 5 S 45 5.16 5 C 22073 2.51 5 N 4821 2.21 5 O 5012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 3": "OE1" <-> "OE2" Residue "C GLU 33": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C GLU 219": "OE1" <-> "OE2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C GLU 327": "OE1" <-> "OE2" Residue "L GLU 6": "OE1" <-> "OE2" Residue "L GLU 104": "OE1" <-> "OE2" Residue "L GLU 210": "OE1" <-> "OE2" Residue "M GLU 22": "OE1" <-> "OE2" Residue "M GLU 244": "OE1" <-> "OE2" Residue "M GLU 261": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H GLU 119": "OE1" <-> "OE2" Residue "H GLU 164": "OE1" <-> "OE2" Residue "H GLU 177": "OE1" <-> "OE2" Residue "H GLU 184": "OE1" <-> "OE2" Residue "H GLU 234": "OE1" <-> "OE2" Residue "H GLU 235": "OE1" <-> "OE2" Residue "H GLU 255": "OE1" <-> "OE2" Residue "z ARG 19": "NH1" <-> "NH2" Residue "1 GLU 12": "OE1" <-> "OE2" Residue "1 GLU 13": "OE1" <-> "OE2" Residue "1 GLU 17": "OE1" <-> "OE2" Residue "2 ARG 36": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "K ARG 19": "NH1" <-> "NH2" Residue "P ARG 19": "NH1" <-> "NH2" Residue "P GLU 49": "OE1" <-> "OE2" Residue "S ARG 19": "NH1" <-> "NH2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "Y ARG 19": "NH1" <-> "NH2" Residue "Y GLU 49": "OE1" <-> "OE2" Residue "b ARG 19": "NH1" <-> "NH2" Residue "e ARG 19": "NH1" <-> "NH2" Residue "e GLU 49": "OE1" <-> "OE2" Residue "h ARG 19": "NH1" <-> "NH2" Residue "h GLU 49": "OE1" <-> "OE2" Residue "k ARG 19": "NH1" <-> "NH2" Residue "n ARG 19": "NH1" <-> "NH2" Residue "n GLU 49": "OE1" <-> "OE2" Residue "q ARG 19": "NH1" <-> "NH2" Residue "t ARG 19": "NH1" <-> "NH2" Residue "w ARG 19": "NH1" <-> "NH2" Residue "w GLU 49": "OE1" <-> "OE2" Residue "3 ARG 19": "NH1" <-> "NH2" Residue "3 GLU 49": "OE1" <-> "OE2" Residue "6 ARG 19": "NH1" <-> "NH2" Residue "6 GLU 49": "OE1" <-> "OE2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "N GLU 13": "OE1" <-> "OE2" Residue "Q GLU 12": "OE1" <-> "OE2" Residue "Q GLU 13": "OE1" <-> "OE2" Residue "T GLU 13": "OE1" <-> "OE2" Residue "W GLU 13": "OE1" <-> "OE2" Residue "Z GLU 13": "OE1" <-> "OE2" Residue "c GLU 12": "OE1" <-> "OE2" Residue "c GLU 13": "OE1" <-> "OE2" Residue "f GLU 12": "OE1" <-> "OE2" Residue "f GLU 13": "OE1" <-> "OE2" Residue "i GLU 13": "OE1" <-> "OE2" Residue "l GLU 13": "OE1" <-> "OE2" Residue "o GLU 12": "OE1" <-> "OE2" Residue "o GLU 13": "OE1" <-> "OE2" Residue "r GLU 12": "OE1" <-> "OE2" Residue "r GLU 13": "OE1" <-> "OE2" Residue "u GLU 12": "OE1" <-> "OE2" Residue "u GLU 13": "OE1" <-> "OE2" Residue "x GLU 12": "OE1" <-> "OE2" Residue "x GLU 13": "OE1" <-> "OE2" Residue "4 GLU 12": "OE1" <-> "OE2" Residue "4 GLU 13": "OE1" <-> "OE2" Residue "7 GLU 12": "OE1" <-> "OE2" Residue "7 GLU 13": "OE1" <-> "OE2" Residue "I ARG 36": "NH1" <-> "NH2" Residue "O ARG 36": "NH1" <-> "NH2" Residue "R ARG 36": "NH1" <-> "NH2" Residue "U ARG 36": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "a ARG 36": "NH1" <-> "NH2" Residue "d ARG 36": "NH1" <-> "NH2" Residue "g ARG 36": "NH1" <-> "NH2" Residue "j ARG 36": "NH1" <-> "NH2" Residue "m ARG 36": "NH1" <-> "NH2" Residue "p ARG 36": "NH1" <-> "NH2" Residue "s ARG 36": "NH1" <-> "NH2" Residue "v ARG 36": "NH1" <-> "NH2" Residue "y ARG 36": "NH1" <-> "NH2" Residue "5 ARG 36": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31994 Number of models: 1 Model: "" Number of chains: 92 Chain: "C" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2603 Classifications: {'peptide': 333} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 305} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2171 Classifications: {'peptide': 273} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain: "M" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2555 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 303} Chain: "H" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2018 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 239} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "1" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "2" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "F" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "K" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "P" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "S" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "V" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "Y" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "b" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "e" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "h" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "k" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "n" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "q" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "t" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "w" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "3" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "6" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "Q" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "T" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "W" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "Z" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "c" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "f" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "i" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "l" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "o" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "r" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "u" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "x" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "4" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "7" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "I" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "O" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "R" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "U" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "X" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "a" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "d" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "g" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "j" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "m" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "p" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "s" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "v" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "y" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "5" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "C" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {'HEM': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 256 Unusual residues: {' FE': 1, 'BCB': 2, 'BPB': 1, 'UQ9': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 331 Unusual residues: {'BCB': 2, 'BPB': 1, 'LDA': 1, 'MQ9': 1, 'NS5': 1, 'SO4': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 31 Unusual residues: {'LDA': 1, 'SO4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "z" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 124 Unusual residues: {'BCB': 1, 'UQ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "o" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "r" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "u" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.86, per 1000 atoms: 0.53 Number of scatterers: 31994 At special positions: 0 Unit cell: (145.22, 145.22, 147.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 5 26.01 S 45 16.00 Mg 38 11.99 O 5012 8.00 N 4821 7.00 C 22073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=60, symmetry=0 Number of additional bonds: simple=60, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.37 Conformation dependent library (CDL) restraints added in 4.9 seconds 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6526 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 123 helices and 5 sheets defined 53.0% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.68 Creating SS restraints... Processing helix chain 'C' and resid 25 through 36 removed outlier: 3.659A pdb=" N ALA C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 55 No H-bonds generated for 'chain 'C' and resid 52 through 55' Processing helix chain 'C' and resid 67 through 81 Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 102 through 120 removed outlier: 3.605A pdb=" N ARG C 109 " --> pdb=" O VAL C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 125 No H-bonds generated for 'chain 'C' and resid 122 through 125' Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 169 through 180 removed outlier: 3.608A pdb=" N TYR C 172 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL C 173 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS C 178 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 193 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 224 through 240 Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 257 through 259 No H-bonds generated for 'chain 'C' and resid 257 through 259' Processing helix chain 'C' and resid 262 through 280 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 315 through 318 Processing helix chain 'L' and resid 7 through 9 No H-bonds generated for 'chain 'L' and resid 7 through 9' Processing helix chain 'L' and resid 19 through 22 No H-bonds generated for 'chain 'L' and resid 19 through 22' Processing helix chain 'L' and resid 32 through 54 Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 84 through 111 Processing helix chain 'L' and resid 116 through 132 removed outlier: 3.691A pdb=" N VAL L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) Proline residue: L 124 - end of helix Processing helix chain 'L' and resid 134 through 139 Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 150 through 163 removed outlier: 4.034A pdb=" N LEU L 154 " --> pdb=" O ILE L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 169 No H-bonds generated for 'chain 'L' and resid 167 through 169' Processing helix chain 'L' and resid 171 through 198 Processing helix chain 'L' and resid 209 through 219 Processing helix chain 'L' and resid 226 through 253 removed outlier: 4.012A pdb=" N HIS L 230 " --> pdb=" O ALA L 226 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE L 241 " --> pdb=" O ALA L 237 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE L 246 " --> pdb=" O LEU L 242 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY L 247 " --> pdb=" O THR L 243 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLY L 252 " --> pdb=" O THR L 248 " (cutoff:3.500A) Proline residue: L 253 - end of helix Processing helix chain 'L' and resid 259 through 267 removed outlier: 4.057A pdb=" N TRP L 263 " --> pdb=" O TRP L 259 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY L 264 " --> pdb=" O PRO L 260 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N TRP L 265 " --> pdb=" O GLU L 261 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TRP L 266 " --> pdb=" O TRP L 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 40 No H-bonds generated for 'chain 'M' and resid 38 through 40' Processing helix chain 'M' and resid 52 through 77 removed outlier: 3.569A pdb=" N VAL M 77 " --> pdb=" O MET M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 90 removed outlier: 6.084A pdb=" N PHE M 89 " --> pdb=" O PHE M 85 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TRP M 90 " --> pdb=" O ARG M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 138 Processing helix chain 'M' and resid 143 through 159 removed outlier: 3.504A pdb=" N ALA M 151 " --> pdb=" O ASN M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 166 Processing helix chain 'M' and resid 169 through 171 No H-bonds generated for 'chain 'M' and resid 169 through 171' Processing helix chain 'M' and resid 177 through 190 removed outlier: 3.643A pdb=" N ILE M 181 " --> pdb=" O ILE M 177 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU M 184 " --> pdb=" O HIS M 180 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR M 185 " --> pdb=" O ILE M 181 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 196 No H-bonds generated for 'chain 'M' and resid 194 through 196' Processing helix chain 'M' and resid 198 through 227 removed outlier: 4.696A pdb=" N ARG M 226 " --> pdb=" O LEU M 222 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE M 227 " --> pdb=" O ALA M 223 " (cutoff:3.500A) Processing helix chain 'M' and resid 232 through 237 Processing helix chain 'M' and resid 241 through 254 Processing helix chain 'M' and resid 260 through 284 removed outlier: 4.313A pdb=" N HIS M 264 " --> pdb=" O ILE M 260 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG M 265 " --> pdb=" O GLU M 261 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET M 275 " --> pdb=" O SER M 271 " (cutoff:3.500A) Processing helix chain 'M' and resid 292 through 298 Processing helix chain 'M' and resid 315 through 317 No H-bonds generated for 'chain 'M' and resid 315 through 317' Processing helix chain 'H' and resid 12 through 30 removed outlier: 3.715A pdb=" N TYR H 18 " --> pdb=" O GLN H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 38 removed outlier: 3.842A pdb=" N ARG H 37 " --> pdb=" O ARG H 33 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG H 38 " --> pdb=" O ARG H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 110 No H-bonds generated for 'chain 'H' and resid 107 through 110' Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'H' and resid 215 through 220 removed outlier: 3.624A pdb=" N ALA H 219 " --> pdb=" O GLU H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 248 removed outlier: 3.742A pdb=" N TYR H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU H 247 " --> pdb=" O ALA H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 253 No H-bonds generated for 'chain 'H' and resid 251 through 253' Processing helix chain 'z' and resid 8 through 15 removed outlier: 4.149A pdb=" N LEU z 15 " --> pdb=" O TRP z 12 " (cutoff:3.500A) Processing helix chain 'z' and resid 17 through 41 Processing helix chain '1' and resid 17 through 42 removed outlier: 3.552A pdb=" N THR 1 42 " --> pdb=" O TYR 1 38 " (cutoff:3.500A) Processing helix chain '2' and resid 19 through 34 Proline residue: 2 27 - end of helix Processing helix chain 'F' and resid 8 through 15 removed outlier: 3.627A pdb=" N LEU F 15 " --> pdb=" O TRP F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 41 Processing helix chain 'K' and resid 8 through 15 removed outlier: 3.797A pdb=" N LEU K 15 " --> pdb=" O TRP K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 41 Processing helix chain 'P' and resid 8 through 15 removed outlier: 3.900A pdb=" N LEU P 15 " --> pdb=" O TRP P 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 41 Processing helix chain 'S' and resid 8 through 14 Processing helix chain 'S' and resid 17 through 41 Processing helix chain 'V' and resid 8 through 15 removed outlier: 3.811A pdb=" N LEU V 15 " --> pdb=" O TRP V 12 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 41 Processing helix chain 'Y' and resid 8 through 15 removed outlier: 3.990A pdb=" N LEU Y 15 " --> pdb=" O TRP Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 41 Processing helix chain 'b' and resid 8 through 14 Processing helix chain 'b' and resid 17 through 41 Processing helix chain 'e' and resid 8 through 15 removed outlier: 3.975A pdb=" N LEU e 15 " --> pdb=" O TRP e 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 17 through 41 Processing helix chain 'h' and resid 8 through 14 Processing helix chain 'h' and resid 17 through 41 Processing helix chain 'k' and resid 8 through 15 removed outlier: 3.685A pdb=" N LEU k 15 " --> pdb=" O TRP k 12 " (cutoff:3.500A) Processing helix chain 'k' and resid 17 through 41 Processing helix chain 'n' and resid 8 through 15 removed outlier: 3.761A pdb=" N LEU n 15 " --> pdb=" O TRP n 12 " (cutoff:3.500A) Processing helix chain 'n' and resid 17 through 41 Processing helix chain 'q' and resid 8 through 15 removed outlier: 3.916A pdb=" N LEU q 15 " --> pdb=" O TRP q 12 " (cutoff:3.500A) Processing helix chain 'q' and resid 17 through 41 Processing helix chain 't' and resid 8 through 15 removed outlier: 3.576A pdb=" N LEU t 15 " --> pdb=" O TRP t 12 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 41 Processing helix chain 'w' and resid 8 through 15 removed outlier: 3.815A pdb=" N LEU w 15 " --> pdb=" O TRP w 12 " (cutoff:3.500A) Processing helix chain 'w' and resid 17 through 41 Processing helix chain '3' and resid 8 through 15 removed outlier: 3.969A pdb=" N LEU 3 15 " --> pdb=" O TRP 3 12 " (cutoff:3.500A) Processing helix chain '3' and resid 17 through 41 Processing helix chain '6' and resid 8 through 15 removed outlier: 3.924A pdb=" N LEU 6 15 " --> pdb=" O TRP 6 12 " (cutoff:3.500A) Processing helix chain '6' and resid 17 through 41 removed outlier: 3.846A pdb=" N ALA 6 23 " --> pdb=" O ARG 6 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 43 Processing helix chain 'N' and resid 17 through 43 Processing helix chain 'Q' and resid 17 through 43 Processing helix chain 'T' and resid 17 through 43 removed outlier: 3.540A pdb=" N ALA T 43 " --> pdb=" O LEU T 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 43 removed outlier: 3.572A pdb=" N LEU W 30 " --> pdb=" O THR W 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 43 Processing helix chain 'c' and resid 17 through 43 Processing helix chain 'f' and resid 17 through 43 Processing helix chain 'i' and resid 17 through 43 Processing helix chain 'l' and resid 17 through 43 Processing helix chain 'o' and resid 17 through 43 Processing helix chain 'r' and resid 17 through 41 Processing helix chain 'u' and resid 17 through 43 Processing helix chain 'x' and resid 17 through 43 removed outlier: 3.602A pdb=" N THR x 42 " --> pdb=" O TYR x 38 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA x 43 " --> pdb=" O LEU x 39 " (cutoff:3.500A) Processing helix chain '4' and resid 17 through 43 removed outlier: 3.546A pdb=" N ALA 4 43 " --> pdb=" O LEU 4 39 " (cutoff:3.500A) Processing helix chain '7' and resid 17 through 43 removed outlier: 3.647A pdb=" N ALA 7 43 " --> pdb=" O LEU 7 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 34 Proline residue: I 27 - end of helix Processing helix chain 'O' and resid 19 through 34 Proline residue: O 27 - end of helix Processing helix chain 'R' and resid 19 through 34 Proline residue: R 27 - end of helix Processing helix chain 'U' and resid 19 through 34 Proline residue: U 27 - end of helix Processing helix chain 'X' and resid 19 through 34 Proline residue: X 27 - end of helix Processing helix chain 'a' and resid 19 through 34 Proline residue: a 27 - end of helix Processing helix chain 'd' and resid 19 through 34 Proline residue: d 27 - end of helix Processing helix chain 'g' and resid 19 through 34 Proline residue: g 27 - end of helix Processing helix chain 'j' and resid 19 through 34 Proline residue: j 27 - end of helix Processing helix chain 'm' and resid 19 through 34 Proline residue: m 27 - end of helix Processing helix chain 'p' and resid 19 through 34 Proline residue: p 27 - end of helix Processing helix chain 's' and resid 19 through 34 Proline residue: s 27 - end of helix Processing helix chain 'v' and resid 19 through 34 Proline residue: v 27 - end of helix Processing helix chain 'y' and resid 19 through 34 Proline residue: y 27 - end of helix Processing helix chain '5' and resid 19 through 34 Proline residue: 5 27 - end of helix Processing sheet with id= A, first strand: chain 'C' and resid 7 through 9 Processing sheet with id= B, first strand: chain 'H' and resid 66 through 69 Processing sheet with id= C, first strand: chain 'H' and resid 90 through 92 Processing sheet with id= D, first strand: chain 'H' and resid 134 through 136 removed outlier: 6.679A pdb=" N GLU H 184 " --> pdb=" O THR H 169 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU H 171 " --> pdb=" O TYR H 182 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TYR H 182 " --> pdb=" O LEU H 171 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG H 192 " --> pdb=" O VAL H 187 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 207 through 209 removed outlier: 3.641A pdb=" N GLY H 166 " --> pdb=" O VAL H 157 " (cutoff:3.500A) 1307 hydrogen bonds defined for protein. 3684 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: 8.70 Time building geometry restraints manager: 15.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 9597 1.37 - 1.55: 22726 1.55 - 1.73: 703 1.73 - 1.90: 62 1.90 - 2.08: 164 Bond restraints: 33252 Sorted by residual: bond pdb=" CAB BCB q 101 " pdb=" CBB BCB q 101 " ideal model delta sigma weight residual 1.510 1.209 0.301 2.30e-02 1.89e+03 1.71e+02 bond pdb=" C2 UQ9 L 304 " pdb=" O2 UQ9 L 304 " ideal model delta sigma weight residual 1.213 1.426 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C2 UQ9 6 101 " pdb=" O2 UQ9 6 101 " ideal model delta sigma weight residual 1.213 1.423 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C28 UQ9 L 304 " pdb=" C29 UQ9 L 304 " ideal model delta sigma weight residual 1.335 1.534 -0.199 2.00e-02 2.50e+03 9.90e+01 bond pdb=" C48 UQ9 L 304 " pdb=" C49 UQ9 L 304 " ideal model delta sigma weight residual 1.336 1.534 -0.198 2.00e-02 2.50e+03 9.79e+01 ... (remaining 33247 not shown) Histogram of bond angle deviations from ideal: 87.40 - 105.86: 1755 105.86 - 124.33: 40727 124.33 - 142.80: 3419 142.80 - 161.26: 32 161.26 - 179.73: 84 Bond angle restraints: 46017 Sorted by residual: angle pdb=" C TRP P 48 " pdb=" CA TRP P 48 " pdb=" CB TRP P 48 " ideal model delta sigma weight residual 111.82 97.11 14.71 1.28e+00 6.10e-01 1.32e+02 angle pdb=" C TRP e 48 " pdb=" CA TRP e 48 " pdb=" CB TRP e 48 " ideal model delta sigma weight residual 111.82 97.36 14.46 1.28e+00 6.10e-01 1.28e+02 angle pdb=" C TRP b 48 " pdb=" CA TRP b 48 " pdb=" CB TRP b 48 " ideal model delta sigma weight residual 111.73 96.55 15.18 1.42e+00 4.96e-01 1.14e+02 angle pdb=" N TYR L 164 " pdb=" CA TYR L 164 " pdb=" C TYR L 164 " ideal model delta sigma weight residual 110.17 93.58 16.59 1.61e+00 3.86e-01 1.06e+02 angle pdb=" N ILE G 47 " pdb=" CA ILE G 47 " pdb=" C ILE G 47 " ideal model delta sigma weight residual 110.42 119.83 -9.41 9.60e-01 1.09e+00 9.60e+01 ... (remaining 46012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 16812 35.58 - 71.15: 955 71.15 - 106.73: 124 106.73 - 142.31: 25 142.31 - 177.88: 9 Dihedral angle restraints: 17925 sinusoidal: 7827 harmonic: 10098 Sorted by residual: dihedral pdb=" CBD BCB 6 102 " pdb=" CGD BCB 6 102 " pdb=" O2D BCB 6 102 " pdb=" CED BCB 6 102 " ideal model delta sinusoidal sigma weight residual -180.00 -59.22 -120.78 1 5.00e+00 4.00e-02 5.81e+02 dihedral pdb=" C1 BCB u 101 " pdb=" CGA BCB u 101 " pdb=" O2A BCB u 101 " pdb=" CBA BCB u 101 " ideal model delta sinusoidal sigma weight residual -180.00 -2.12 -177.88 1 6.00e+00 2.78e-02 5.33e+02 dihedral pdb=" C1 BCB i 101 " pdb=" CGA BCB i 101 " pdb=" O2A BCB i 101 " pdb=" CBA BCB i 101 " ideal model delta sinusoidal sigma weight residual 180.00 2.81 177.19 1 6.00e+00 2.78e-02 5.33e+02 ... (remaining 17922 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.045: 4798 1.045 - 2.089: 13 2.089 - 3.134: 0 3.134 - 4.178: 0 4.178 - 5.223: 2 Chirality restraints: 4813 Sorted by residual: chirality pdb=" C13 BPB M 407 " pdb=" C12 BPB M 407 " pdb=" C14 BPB M 407 " pdb=" C15 BPB M 407 " both_signs ideal model delta sigma weight residual False 2.60 -2.63 5.22 2.00e-01 2.50e+01 6.82e+02 chirality pdb=" C13 BPB L 303 " pdb=" C12 BPB L 303 " pdb=" C14 BPB L 303 " pdb=" C15 BPB L 303 " both_signs ideal model delta sigma weight residual False 2.60 -2.54 5.13 2.00e-01 2.50e+01 6.59e+02 chirality pdb=" CA LEU P 40 " pdb=" N LEU P 40 " pdb=" C LEU P 40 " pdb=" CB LEU P 40 " both_signs ideal model delta sigma weight residual False 2.51 1.19 1.32 2.00e-01 2.50e+01 4.34e+01 ... (remaining 4810 not shown) Planarity restraints: 5558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 6 101 " 0.144 2.00e-02 2.50e+03 2.58e-01 1.99e+03 pdb=" C1M UQ9 6 101 " 0.227 2.00e-02 2.50e+03 pdb=" C2 UQ9 6 101 " 0.254 2.00e-02 2.50e+03 pdb=" C3 UQ9 6 101 " 0.153 2.00e-02 2.50e+03 pdb=" C4 UQ9 6 101 " 0.043 2.00e-02 2.50e+03 pdb=" C5 UQ9 6 101 " -0.051 2.00e-02 2.50e+03 pdb=" C6 UQ9 6 101 " 0.004 2.00e-02 2.50e+03 pdb=" C7 UQ9 6 101 " -0.040 2.00e-02 2.50e+03 pdb=" O2 UQ9 6 101 " -0.738 2.00e-02 2.50e+03 pdb=" O3 UQ9 6 101 " 0.230 2.00e-02 2.50e+03 pdb=" O4 UQ9 6 101 " -0.053 2.00e-02 2.50e+03 pdb=" O5 UQ9 6 101 " -0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 L 304 " 0.152 2.00e-02 2.50e+03 2.56e-01 1.97e+03 pdb=" C1M UQ9 L 304 " 0.224 2.00e-02 2.50e+03 pdb=" C2 UQ9 L 304 " 0.253 2.00e-02 2.50e+03 pdb=" C3 UQ9 L 304 " 0.144 2.00e-02 2.50e+03 pdb=" C4 UQ9 L 304 " 0.020 2.00e-02 2.50e+03 pdb=" C5 UQ9 L 304 " -0.051 2.00e-02 2.50e+03 pdb=" C6 UQ9 L 304 " 0.035 2.00e-02 2.50e+03 pdb=" C7 UQ9 L 304 " -0.059 2.00e-02 2.50e+03 pdb=" O2 UQ9 L 304 " -0.733 2.00e-02 2.50e+03 pdb=" O3 UQ9 L 304 " 0.229 2.00e-02 2.50e+03 pdb=" O4 UQ9 L 304 " -0.044 2.00e-02 2.50e+03 pdb=" O5 UQ9 L 304 " -0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA NS0 i 102 " 0.295 2.00e-02 2.50e+03 3.23e-01 1.30e+03 pdb=" CB NS0 i 102 " -0.589 2.00e-02 2.50e+03 pdb=" CG NS0 i 102 " 0.293 2.00e-02 2.50e+03 pdb=" CD1 NS0 i 102 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 NS0 i 102 " -0.006 2.00e-02 2.50e+03 ... (remaining 5555 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 32 2.25 - 2.92: 13089 2.92 - 3.58: 46884 3.58 - 4.24: 80956 4.24 - 4.90: 130193 Nonbonded interactions: 271154 Sorted by model distance: nonbonded pdb=" CD1 ILE f 47 " pdb=" CD1 LEU d 17 " model vdw 1.592 3.880 nonbonded pdb=" CD1 ILE N 47 " pdb=" CD1 LEU I 17 " model vdw 1.701 3.880 nonbonded pdb=" O TRP L 25 " pdb=" NH2 ARG 3 19 " model vdw 1.791 2.520 nonbonded pdb=" CG1 ILE 1 21 " pdb=" C8 NS0 1 102 " model vdw 1.856 3.088 nonbonded pdb=" O ALA 6 23 " pdb=" CD2 TYR 6 27 " model vdw 1.863 3.340 ... (remaining 271149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '1' selection = chain '4' selection = chain '7' selection = chain 'G' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'c' selection = chain 'f' selection = chain 'i' selection = chain 'l' selection = chain 'o' selection = chain 'r' selection = chain 'u' selection = chain 'x' } ncs_group { reference = chain '2' selection = chain '5' selection = chain 'I' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'd' selection = chain 'g' selection = chain 'j' selection = chain 'm' selection = chain 'p' selection = chain 's' selection = chain 'v' selection = chain 'y' } ncs_group { reference = (chain '3' and resid 1 through 58) selection = (chain '6' and resid 1 through 58) selection = (chain 'F' and resid 1 through 58) selection = (chain 'K' and resid 1 through 58) selection = (chain 'P' and resid 1 through 58) selection = (chain 'S' and resid 1 through 58) selection = (chain 'V' and resid 1 through 58) selection = (chain 'Y' and resid 1 through 58) selection = (chain 'b' and resid 1 through 58) selection = (chain 'e' and resid 1 through 58) selection = (chain 'h' and resid 1 through 58) selection = (chain 'k' and resid 1 through 58) selection = (chain 'n' and resid 1 through 58) selection = (chain 'q' and resid 1 through 58) selection = (chain 't' and resid 1 through 58) selection = (chain 'w' and resid 1 through 58) selection = (chain 'z' and resid 1 through 58) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 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: 4.520 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 80.830 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.600 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: 0.020 Load rotamer database and sin/cos tables:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 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 : 0.025 0.301 33252 Z= 1.347 Angle : 2.859 26.570 46017 Z= 1.477 Chirality : 0.206 5.223 4813 Planarity : 0.029 0.350 5558 Dihedral : 21.889 177.884 11399 Min Nonbonded Distance : 1.592 Molprobity Statistics. All-atom Clashscore : 33.46 Ramachandran Plot: Outliers : 4.08 % Allowed : 12.22 % Favored : 83.70 % Rotamer: Outliers : 8.13 % Allowed : 12.88 % Favored : 79.00 % Cbeta Deviations : 6.19 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 1.42 % Twisted General : 1.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.05 (0.11), residues: 3380 helix: -2.60 (0.09), residues: 1693 sheet: -2.28 (0.87), residues: 26 loop : -4.33 (0.12), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.007 TRP L 86 HIS 0.019 0.004 HIS L 230 PHE 0.045 0.005 PHE L 62 TYR 0.056 0.005 TYR C 227 ARG 0.015 0.001 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 713 time to evaluate : 2.794 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: C 74 MET cc_start: 0.9558 (mmp) cc_final: 0.9288 (mmt) REVERT: C 110 MET cc_start: 0.9562 (mmt) cc_final: 0.9159 (mmt) REVERT: C 113 MET cc_start: 0.9602 (ttp) cc_final: 0.9343 (ttp) REVERT: C 123 GLN cc_start: 0.9482 (OUTLIER) cc_final: 0.9254 (pm20) REVERT: C 233 MET cc_start: 0.9340 (mmp) cc_final: 0.8443 (mmt) REVERT: C 252 THR cc_start: 0.9671 (OUTLIER) cc_final: 0.9464 (p) REVERT: L 23 ASP cc_start: 0.9598 (t0) cc_final: 0.9271 (t0) REVERT: L 106 GLU cc_start: 0.9754 (mt-10) cc_final: 0.9545 (mm-30) REVERT: L 204 ASP cc_start: 0.9350 (m-30) cc_final: 0.9107 (m-30) REVERT: L 228 SER cc_start: 0.9564 (OUTLIER) cc_final: 0.9272 (p) REVERT: M 244 GLU cc_start: 0.9367 (mt-10) cc_final: 0.9020 (mm-30) REVERT: H 133 LYS cc_start: 0.9616 (OUTLIER) cc_final: 0.9324 (ttmp) REVERT: H 161 ASP cc_start: 0.9380 (OUTLIER) cc_final: 0.8716 (p0) REVERT: H 217 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8564 (pm20) REVERT: H 237 LYS cc_start: 0.9674 (OUTLIER) cc_final: 0.9384 (mmtp) REVERT: H 239 SER cc_start: 0.9859 (m) cc_final: 0.9623 (p) REVERT: 2 34 THR cc_start: 0.9477 (m) cc_final: 0.9249 (p) REVERT: F 31 ILE cc_start: 0.9722 (OUTLIER) cc_final: 0.9424 (pp) REVERT: F 44 ARG cc_start: 0.9439 (OUTLIER) cc_final: 0.8727 (ttt-90) REVERT: K 18 ARG cc_start: 0.9333 (mtm110) cc_final: 0.8777 (tmt170) REVERT: b 44 ARG cc_start: 0.9500 (OUTLIER) cc_final: 0.8943 (mtm180) REVERT: h 43 ASP cc_start: 0.9780 (m-30) cc_final: 0.9482 (m-30) REVERT: h 51 GLN cc_start: 0.9537 (tp40) cc_final: 0.9330 (mm-40) REVERT: k 56 LYS cc_start: 0.9319 (tmtp) cc_final: 0.9008 (mppt) REVERT: w 52 ARG cc_start: 0.9348 (mtm-85) cc_final: 0.9078 (ppt170) REVERT: 3 16 ASP cc_start: 0.9333 (t0) cc_final: 0.8688 (t0) REVERT: 3 27 TYR cc_start: 0.9342 (t80) cc_final: 0.9118 (t80) REVERT: 3 44 ARG cc_start: 0.9473 (OUTLIER) cc_final: 0.9243 (mtp-110) REVERT: 6 4 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.7339 (m-10) REVERT: c 44 ARG cc_start: 0.9497 (OUTLIER) cc_final: 0.9264 (mmp80) REVERT: l 29 TYR cc_start: 0.9512 (t80) cc_final: 0.9279 (t80) REVERT: o 16 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8802 (ptpt) REVERT: r 16 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8930 (mttp) REVERT: d 16 ASN cc_start: 0.6804 (OUTLIER) cc_final: 0.6364 (t0) REVERT: s 35 TYR cc_start: 0.9453 (m-80) cc_final: 0.8938 (m-10) outliers start: 238 outliers final: 56 residues processed: 873 average time/residue: 1.0975 time to fit residues: 1176.2577 Evaluate side-chains 536 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 464 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain L residue 228 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 194 PHE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain H residue 237 LYS Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain b residue 44 ARG Chi-restraints excluded: chain w residue 19 ARG Chi-restraints excluded: chain w residue 21 LEU Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 44 ARG Chi-restraints excluded: chain 6 residue 4 TYR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 14 GLU Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain Z residue 14 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 14 GLU Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 44 ARG Chi-restraints excluded: chain f residue 13 GLU Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 27 VAL Chi-restraints excluded: chain i residue 14 GLU Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain l residue 14 GLU Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 16 LYS Chi-restraints excluded: chain o residue 25 SER Chi-restraints excluded: chain o residue 34 VAL Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain r residue 23 VAL Chi-restraints excluded: chain r residue 36 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain u residue 14 GLU Chi-restraints excluded: chain u residue 23 VAL Chi-restraints excluded: chain x residue 14 GLU Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain 4 residue 34 VAL Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 14 GLU Chi-restraints excluded: chain 7 residue 34 VAL Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain d residue 16 ASN Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain s residue 17 LEU Chi-restraints excluded: chain s residue 26 ILE Chi-restraints excluded: chain y residue 14 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 269 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 250 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 289 optimal weight: 8.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 GLN L 144 HIS L 211 HIS L 239 ASN H 58 GLN H 106 ASN ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 46 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 33252 Z= 0.344 Angle : 1.126 19.574 46017 Z= 0.491 Chirality : 0.053 0.905 4813 Planarity : 0.006 0.074 5558 Dihedral : 20.626 179.907 5348 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.96 % Favored : 90.33 % Rotamer: Outliers : 5.70 % Allowed : 23.26 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.14), residues: 3380 helix: 0.32 (0.11), residues: 1760 sheet: 0.04 (1.08), residues: 22 loop : -3.79 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP O 15 HIS 0.010 0.001 HIS L 153 PHE 0.024 0.002 PHE 7 18 TYR 0.018 0.002 TYR 6 27 ARG 0.012 0.001 ARG b 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 572 time to evaluate : 3.546 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: C 37 GLN cc_start: 0.9414 (OUTLIER) cc_final: 0.8979 (mp10) REVERT: C 110 MET cc_start: 0.9415 (mmt) cc_final: 0.8919 (mmt) REVERT: C 113 MET cc_start: 0.9635 (ttp) cc_final: 0.9384 (ttp) REVERT: C 149 GLU cc_start: 0.9394 (OUTLIER) cc_final: 0.9169 (pm20) REVERT: C 252 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8971 (p) REVERT: L 23 ASP cc_start: 0.9561 (t0) cc_final: 0.9032 (t0) REVERT: M 9 GLN cc_start: 0.9348 (mt0) cc_final: 0.9131 (mt0) REVERT: M 22 GLU cc_start: 0.9588 (tm-30) cc_final: 0.9304 (tm-30) REVERT: M 171 GLU cc_start: 0.9606 (OUTLIER) cc_final: 0.8885 (mt-10) REVERT: M 193 ASN cc_start: 0.9420 (t0) cc_final: 0.9039 (t0) REVERT: H 66 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8685 (mtpt) REVERT: H 92 GLN cc_start: 0.9201 (pm20) cc_final: 0.8931 (pm20) REVERT: H 161 ASP cc_start: 0.9394 (OUTLIER) cc_final: 0.8837 (p0) REVERT: H 204 LYS cc_start: 0.8387 (mmmm) cc_final: 0.8170 (mmmm) REVERT: H 217 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8762 (pm20) REVERT: H 239 SER cc_start: 0.9853 (m) cc_final: 0.9617 (p) REVERT: K 18 ARG cc_start: 0.9401 (mtm110) cc_final: 0.8956 (tmt170) REVERT: P 43 ASP cc_start: 0.9451 (m-30) cc_final: 0.9152 (t0) REVERT: e 51 GLN cc_start: 0.9602 (mm-40) cc_final: 0.9275 (mm-40) REVERT: q 25 PHE cc_start: 0.9375 (t80) cc_final: 0.9153 (t80) REVERT: q 27 TYR cc_start: 0.9403 (t80) cc_final: 0.9202 (t80) REVERT: 3 44 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8462 (mtm180) REVERT: 6 51 GLN cc_start: 0.9379 (mm-40) cc_final: 0.9130 (tp-100) REVERT: G 13 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7733 (pp20) REVERT: Q 16 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8993 (pmmt) REVERT: W 16 LYS cc_start: 0.9492 (OUTLIER) cc_final: 0.9250 (ptpp) REVERT: l 29 TYR cc_start: 0.9476 (t80) cc_final: 0.9272 (t80) REVERT: r 16 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8937 (mttp) REVERT: O 24 LEU cc_start: 0.9533 (mm) cc_final: 0.9224 (mm) REVERT: g 24 LEU cc_start: 0.9445 (mt) cc_final: 0.9010 (mt) outliers start: 167 outliers final: 46 residues processed: 682 average time/residue: 0.9492 time to fit residues: 823.1841 Evaluate side-chains 527 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 469 time to evaluate : 3.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 171 GLU Chi-restraints excluded: chain M residue 180 HIS Chi-restraints excluded: chain M residue 194 PHE Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain z residue 35 ILE Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 2 residue 24 LEU Chi-restraints excluded: chain P residue 19 ARG Chi-restraints excluded: chain Y residue 4 TYR Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain q residue 47 TRP Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 43 ASP Chi-restraints excluded: chain t residue 45 LEU Chi-restraints excluded: chain 3 residue 16 ASP Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 44 ARG Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 25 SER Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain r residue 27 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain u residue 23 VAL Chi-restraints excluded: chain 4 residue 13 GLU Chi-restraints excluded: chain 4 residue 47 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain v residue 21 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 160 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 241 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 290 optimal weight: 6.9990 chunk 313 optimal weight: 3.9990 chunk 258 optimal weight: 0.5980 chunk 287 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 232 optimal weight: 9.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 214 GLN q 46 ASN 3 46 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33252 Z= 0.272 Angle : 0.986 26.785 46017 Z= 0.424 Chirality : 0.046 0.558 4813 Planarity : 0.005 0.068 5558 Dihedral : 18.528 179.677 5241 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.93 % Favored : 90.68 % Rotamer: Outliers : 4.47 % Allowed : 25.03 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.15), residues: 3380 helix: 1.75 (0.12), residues: 1646 sheet: 0.84 (1.09), residues: 22 loop : -3.07 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP m 30 HIS 0.013 0.001 HIS o 19 PHE 0.020 0.001 PHE 7 18 TYR 0.023 0.001 TYR V 27 ARG 0.010 0.001 ARG V 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 541 time to evaluate : 3.255 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: C 37 GLN cc_start: 0.9410 (OUTLIER) cc_final: 0.8975 (mp10) REVERT: C 110 MET cc_start: 0.9372 (mmt) cc_final: 0.8669 (mmt) REVERT: C 113 MET cc_start: 0.9644 (ttp) cc_final: 0.9284 (ttp) REVERT: C 149 GLU cc_start: 0.9331 (OUTLIER) cc_final: 0.9113 (pm20) REVERT: C 252 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8736 (p) REVERT: L 23 ASP cc_start: 0.9553 (t0) cc_final: 0.9054 (t0) REVERT: L 214 GLN cc_start: 0.9484 (OUTLIER) cc_final: 0.9281 (tp40) REVERT: M 22 GLU cc_start: 0.9602 (tm-30) cc_final: 0.9347 (tm-30) REVERT: M 26 ASN cc_start: 0.9706 (OUTLIER) cc_final: 0.9450 (p0) REVERT: M 193 ASN cc_start: 0.9400 (t0) cc_final: 0.9032 (t0) REVERT: M 244 GLU cc_start: 0.9334 (mt-10) cc_final: 0.8954 (mm-30) REVERT: H 66 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8730 (mtpt) REVERT: H 92 GLN cc_start: 0.9342 (pm20) cc_final: 0.8910 (pm20) REVERT: H 102 GLN cc_start: 0.9160 (mt0) cc_final: 0.8853 (pm20) REVERT: H 161 ASP cc_start: 0.9370 (OUTLIER) cc_final: 0.8918 (p0) REVERT: H 217 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8745 (pm20) REVERT: H 239 SER cc_start: 0.9847 (m) cc_final: 0.9603 (p) REVERT: K 18 ARG cc_start: 0.9425 (mtm110) cc_final: 0.8911 (tmt170) REVERT: P 16 ASP cc_start: 0.9705 (t0) cc_final: 0.9497 (t0) REVERT: S 16 ASP cc_start: 0.9530 (t0) cc_final: 0.9305 (t0) REVERT: Y 16 ASP cc_start: 0.9605 (t0) cc_final: 0.9353 (t0) REVERT: Y 51 GLN cc_start: 0.9366 (mm-40) cc_final: 0.9075 (tp-100) REVERT: h 16 ASP cc_start: 0.9532 (t0) cc_final: 0.9317 (OUTLIER) REVERT: k 56 LYS cc_start: 0.9264 (tppt) cc_final: 0.8797 (mppt) REVERT: n 14 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8842 (tp) REVERT: q 25 PHE cc_start: 0.9371 (t80) cc_final: 0.9168 (t80) REVERT: 3 16 ASP cc_start: 0.9236 (t0) cc_final: 0.9009 (t0) REVERT: 3 43 ASP cc_start: 0.9562 (m-30) cc_final: 0.9306 (m-30) REVERT: 6 51 GLN cc_start: 0.9490 (mm-40) cc_final: 0.9229 (tp-100) REVERT: Z 17 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8651 (pm20) REVERT: r 16 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8718 (ptpt) REVERT: 7 54 TRP cc_start: 0.9498 (OUTLIER) cc_final: 0.8146 (t60) REVERT: d 24 LEU cc_start: 0.9382 (mm) cc_final: 0.9095 (mm) outliers start: 131 outliers final: 40 residues processed: 626 average time/residue: 0.9143 time to fit residues: 731.5062 Evaluate side-chains 530 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 479 time to evaluate : 3.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain L residue 214 GLN Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain M residue 180 HIS Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain P residue 19 ARG Chi-restraints excluded: chain Y residue 4 TYR Chi-restraints excluded: chain e residue 47 TRP Chi-restraints excluded: chain n residue 14 ILE Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain w residue 20 VAL Chi-restraints excluded: chain 3 residue 47 TRP Chi-restraints excluded: chain 6 residue 20 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 13 GLU Chi-restraints excluded: chain 4 residue 25 SER Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 54 TRP Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain s residue 31 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 286 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 150 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 194 optimal weight: 30.0000 chunk 291 optimal weight: 6.9990 chunk 308 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 276 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 4 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 33252 Z= 0.276 Angle : 0.932 19.026 46017 Z= 0.393 Chirality : 0.045 0.309 4813 Planarity : 0.005 0.071 5558 Dihedral : 17.643 179.953 5227 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.47 % Favored : 90.15 % Rotamer: Outliers : 4.20 % Allowed : 25.82 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3380 helix: 2.08 (0.12), residues: 1648 sheet: 0.17 (1.01), residues: 32 loop : -2.91 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP m 30 HIS 0.008 0.001 HIS L 153 PHE 0.025 0.001 PHE 7 22 TYR 0.029 0.001 TYR O 35 ARG 0.015 0.001 ARG S 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 521 time to evaluate : 3.774 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: C 37 GLN cc_start: 0.9427 (OUTLIER) cc_final: 0.8983 (mp10) REVERT: C 110 MET cc_start: 0.9377 (mmt) cc_final: 0.8693 (mmt) REVERT: C 113 MET cc_start: 0.9638 (ttp) cc_final: 0.9404 (ttp) REVERT: C 149 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.9071 (pm20) REVERT: C 252 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8701 (p) REVERT: L 23 ASP cc_start: 0.9537 (t0) cc_final: 0.9051 (t0) REVERT: L 212 GLU cc_start: 0.9602 (pt0) cc_final: 0.9385 (pm20) REVERT: M 9 GLN cc_start: 0.9423 (mt0) cc_final: 0.9169 (mt0) REVERT: M 22 GLU cc_start: 0.9608 (tm-30) cc_final: 0.9346 (tm-30) REVERT: M 26 ASN cc_start: 0.9691 (OUTLIER) cc_final: 0.9443 (p0) REVERT: M 193 ASN cc_start: 0.9373 (t0) cc_final: 0.9058 (t0) REVERT: H 66 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8742 (mtpt) REVERT: H 92 GLN cc_start: 0.9369 (pm20) cc_final: 0.8907 (pm20) REVERT: H 102 GLN cc_start: 0.9131 (mt0) cc_final: 0.8858 (pm20) REVERT: H 161 ASP cc_start: 0.9351 (OUTLIER) cc_final: 0.8905 (p0) REVERT: H 217 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8798 (pm20) REVERT: H 239 SER cc_start: 0.9845 (m) cc_final: 0.9591 (p) REVERT: K 18 ARG cc_start: 0.9443 (mtm110) cc_final: 0.8851 (tmt170) REVERT: P 16 ASP cc_start: 0.9645 (t0) cc_final: 0.9396 (t0) REVERT: S 16 ASP cc_start: 0.9485 (t0) cc_final: 0.9238 (t0) REVERT: Y 16 ASP cc_start: 0.9585 (t0) cc_final: 0.9332 (t0) REVERT: Y 51 GLN cc_start: 0.9509 (mm-40) cc_final: 0.9298 (tp-100) REVERT: h 16 ASP cc_start: 0.9506 (t0) cc_final: 0.9234 (OUTLIER) REVERT: k 56 LYS cc_start: 0.9274 (tppt) cc_final: 0.9033 (mppt) REVERT: n 3 GLU cc_start: 0.8156 (pp20) cc_final: 0.7951 (pm20) REVERT: q 14 ILE cc_start: 0.9146 (tp) cc_final: 0.8723 (tt) REVERT: q 16 ASP cc_start: 0.9190 (t0) cc_final: 0.8960 (t0) REVERT: q 25 PHE cc_start: 0.9396 (t80) cc_final: 0.9189 (t80) REVERT: 3 43 ASP cc_start: 0.9609 (m-30) cc_final: 0.9345 (m-30) REVERT: 6 51 GLN cc_start: 0.9490 (mm-40) cc_final: 0.9279 (tp-100) REVERT: o 13 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: r 16 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8885 (ptpt) REVERT: 7 13 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: d 35 TYR cc_start: 0.9220 (m-80) cc_final: 0.8883 (m-10) REVERT: 5 34 THR cc_start: 0.9741 (OUTLIER) cc_final: 0.9445 (t) outliers start: 123 outliers final: 48 residues processed: 605 average time/residue: 0.9055 time to fit residues: 703.4260 Evaluate side-chains 531 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 473 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 180 HIS Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain P residue 19 ARG Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain Y residue 4 TYR Chi-restraints excluded: chain e residue 47 TRP Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain t residue 43 ASP Chi-restraints excluded: chain w residue 52 ARG Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 51 GLN Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Z residue 13 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 30 LEU Chi-restraints excluded: chain 4 residue 47 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 13 GLU Chi-restraints excluded: chain 7 residue 47 ILE Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain v residue 34 THR Chi-restraints excluded: chain 5 residue 34 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 256 optimal weight: 10.0000 chunk 175 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 229 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 213 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 213 ASN h 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 33252 Z= 0.260 Angle : 0.913 19.395 46017 Z= 0.382 Chirality : 0.044 0.228 4813 Planarity : 0.004 0.056 5558 Dihedral : 17.038 179.806 5227 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.50 % Favored : 90.09 % Rotamer: Outliers : 4.13 % Allowed : 26.06 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 3380 helix: 2.19 (0.12), residues: 1660 sheet: 0.31 (1.04), residues: 32 loop : -2.77 (0.16), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP m 30 HIS 0.007 0.001 HIS L 153 PHE 0.015 0.001 PHE 7 18 TYR 0.027 0.001 TYR s 35 ARG 0.010 0.000 ARG 6 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 516 time to evaluate : 3.596 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: C 37 GLN cc_start: 0.9403 (OUTLIER) cc_final: 0.8951 (mp10) REVERT: C 110 MET cc_start: 0.9363 (mmt) cc_final: 0.8851 (mmt) REVERT: C 252 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8698 (p) REVERT: L 23 ASP cc_start: 0.9536 (t0) cc_final: 0.9031 (t0) REVERT: M 9 GLN cc_start: 0.9444 (mt0) cc_final: 0.9186 (mt0) REVERT: M 22 GLU cc_start: 0.9607 (tm-30) cc_final: 0.9336 (tm-30) REVERT: M 26 ASN cc_start: 0.9675 (OUTLIER) cc_final: 0.9426 (p0) REVERT: M 193 ASN cc_start: 0.9368 (t0) cc_final: 0.9062 (t0) REVERT: H 66 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8727 (mtpt) REVERT: H 92 GLN cc_start: 0.9394 (pm20) cc_final: 0.8972 (pm20) REVERT: H 96 PHE cc_start: 0.7386 (t80) cc_final: 0.7053 (t80) REVERT: H 102 GLN cc_start: 0.9114 (mt0) cc_final: 0.8873 (pm20) REVERT: H 161 ASP cc_start: 0.9341 (OUTLIER) cc_final: 0.8878 (p0) REVERT: H 217 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8778 (pm20) REVERT: H 239 SER cc_start: 0.9841 (m) cc_final: 0.9579 (p) REVERT: K 18 ARG cc_start: 0.9434 (mtm110) cc_final: 0.8866 (tmt170) REVERT: P 16 ASP cc_start: 0.9614 (t0) cc_final: 0.9334 (t0) REVERT: S 16 ASP cc_start: 0.9442 (t0) cc_final: 0.9161 (t0) REVERT: Y 16 ASP cc_start: 0.9567 (t0) cc_final: 0.9306 (t0) REVERT: b 42 THR cc_start: 0.9624 (p) cc_final: 0.9407 (t) REVERT: h 16 ASP cc_start: 0.9458 (t0) cc_final: 0.9165 (t0) REVERT: q 15 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8915 (mm) REVERT: q 16 ASP cc_start: 0.9140 (t0) cc_final: 0.8833 (OUTLIER) REVERT: q 25 PHE cc_start: 0.9405 (t80) cc_final: 0.9191 (t80) REVERT: t 16 ASP cc_start: 0.9359 (t0) cc_final: 0.9113 (t70) REVERT: 3 16 ASP cc_start: 0.9309 (t0) cc_final: 0.8589 (p0) REVERT: 3 43 ASP cc_start: 0.9615 (m-30) cc_final: 0.9365 (m-30) REVERT: 6 16 ASP cc_start: 0.9223 (t0) cc_final: 0.8838 (t0) REVERT: 6 51 GLN cc_start: 0.9530 (mm-40) cc_final: 0.9276 (tp-100) REVERT: u 13 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: 7 13 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: d 34 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.9068 (t) REVERT: j 34 THR cc_start: 0.9639 (OUTLIER) cc_final: 0.9227 (p) outliers start: 121 outliers final: 52 residues processed: 594 average time/residue: 0.8970 time to fit residues: 683.8583 Evaluate side-chains 527 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 465 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 180 HIS Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain P residue 19 ARG Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain Y residue 4 TYR Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain q residue 15 LEU Chi-restraints excluded: chain t residue 43 ASP Chi-restraints excluded: chain 3 residue 51 GLN Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Z residue 13 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 13 GLU Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain f residue 2 ASP Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain i residue 13 GLU Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain u residue 13 GLU Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 13 GLU Chi-restraints excluded: chain 4 residue 47 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 13 GLU Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain p residue 29 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 103 optimal weight: 20.0000 chunk 277 optimal weight: 6.9990 chunk 60 optimal weight: 0.0060 chunk 181 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 308 optimal weight: 9.9990 chunk 256 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 overall best weight: 6.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 33252 Z= 0.409 Angle : 0.981 20.315 46017 Z= 0.412 Chirality : 0.047 0.410 4813 Planarity : 0.005 0.084 5558 Dihedral : 16.856 179.200 5222 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.50 % Favored : 89.05 % Rotamer: Outliers : 4.03 % Allowed : 27.08 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3380 helix: 2.20 (0.12), residues: 1660 sheet: -0.38 (0.98), residues: 36 loop : -2.80 (0.16), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP s 30 HIS 0.010 0.001 HIS L 153 PHE 0.030 0.001 PHE 7 22 TYR 0.028 0.001 TYR V 27 ARG 0.017 0.001 ARG S 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 470 time to evaluate : 3.420 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: C 37 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.8995 (mp10) REVERT: C 252 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8913 (p) REVERT: L 23 ASP cc_start: 0.9583 (t0) cc_final: 0.9050 (t0) REVERT: M 9 GLN cc_start: 0.9449 (mt0) cc_final: 0.9193 (mt0) REVERT: M 22 GLU cc_start: 0.9583 (tm-30) cc_final: 0.9300 (tm-30) REVERT: M 26 ASN cc_start: 0.9677 (OUTLIER) cc_final: 0.9431 (OUTLIER) REVERT: M 193 ASN cc_start: 0.9435 (t0) cc_final: 0.9077 (t0) REVERT: H 66 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8723 (mtpt) REVERT: H 92 GLN cc_start: 0.9409 (pm20) cc_final: 0.8952 (pm20) REVERT: H 102 GLN cc_start: 0.9101 (mt0) cc_final: 0.8867 (pm20) REVERT: H 161 ASP cc_start: 0.9319 (OUTLIER) cc_final: 0.8905 (p0) REVERT: H 209 VAL cc_start: 0.9400 (OUTLIER) cc_final: 0.9180 (p) REVERT: H 217 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8814 (pm20) REVERT: z 16 ASP cc_start: 0.9610 (t0) cc_final: 0.9368 (t0) REVERT: P 16 ASP cc_start: 0.9611 (t0) cc_final: 0.9315 (t0) REVERT: S 16 ASP cc_start: 0.9407 (t0) cc_final: 0.9108 (t0) REVERT: Y 16 ASP cc_start: 0.9567 (t0) cc_final: 0.9313 (t0) REVERT: h 16 ASP cc_start: 0.9417 (t0) cc_final: 0.9094 (t0) REVERT: n 3 GLU cc_start: 0.8135 (pp20) cc_final: 0.7932 (pm20) REVERT: q 16 ASP cc_start: 0.9178 (t0) cc_final: 0.8893 (OUTLIER) REVERT: q 25 PHE cc_start: 0.9434 (t80) cc_final: 0.9208 (t80) REVERT: t 16 ASP cc_start: 0.9432 (t0) cc_final: 0.9195 (t70) REVERT: 3 16 ASP cc_start: 0.9277 (t0) cc_final: 0.8475 (OUTLIER) REVERT: 3 43 ASP cc_start: 0.9691 (m-30) cc_final: 0.9472 (m-30) REVERT: 6 16 ASP cc_start: 0.9335 (t0) cc_final: 0.8982 (t0) REVERT: r 16 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.9065 (mttp) REVERT: d 34 THR cc_start: 0.9668 (t) cc_final: 0.9356 (p) REVERT: v 34 THR cc_start: 0.9789 (t) cc_final: 0.9572 (p) outliers start: 118 outliers final: 60 residues processed: 551 average time/residue: 0.9005 time to fit residues: 639.2320 Evaluate side-chains 507 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 442 time to evaluate : 3.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain L residue 202 ASP Chi-restraints excluded: chain L residue 205 LYS Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 180 HIS Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain z residue 15 LEU Chi-restraints excluded: chain z residue 35 ILE Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain Y residue 4 TYR Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain e residue 47 TRP Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 43 ASP Chi-restraints excluded: chain w residue 52 ARG Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 13 GLU Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain i residue 13 GLU Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 13 GLU Chi-restraints excluded: chain 4 residue 30 LEU Chi-restraints excluded: chain 4 residue 47 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 13 GLU Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain j residue 21 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 297 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 chunk 225 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 259 optimal weight: 0.4980 chunk 172 optimal weight: 0.9980 chunk 307 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 33252 Z= 0.234 Angle : 0.912 18.037 46017 Z= 0.382 Chirality : 0.044 0.249 4813 Planarity : 0.004 0.061 5558 Dihedral : 16.540 179.792 5222 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.05 % Favored : 90.56 % Rotamer: Outliers : 3.35 % Allowed : 28.21 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3380 helix: 2.19 (0.12), residues: 1663 sheet: -0.46 (0.97), residues: 36 loop : -2.68 (0.16), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP m 30 HIS 0.006 0.001 HIS L 153 PHE 0.016 0.001 PHE L 235 TYR 0.028 0.001 TYR V 27 ARG 0.013 0.000 ARG 6 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 512 time to evaluate : 3.454 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: C 37 GLN cc_start: 0.9637 (OUTLIER) cc_final: 0.9109 (mp10) REVERT: C 110 MET cc_start: 0.9465 (mmt) cc_final: 0.8558 (mmt) REVERT: C 252 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8781 (p) REVERT: L 23 ASP cc_start: 0.9496 (t0) cc_final: 0.9100 (t0) REVERT: M 9 GLN cc_start: 0.9468 (mt0) cc_final: 0.9224 (mt0) REVERT: M 22 GLU cc_start: 0.9582 (tm-30) cc_final: 0.9280 (tm-30) REVERT: M 26 ASN cc_start: 0.9683 (OUTLIER) cc_final: 0.9447 (p0) REVERT: M 193 ASN cc_start: 0.9344 (t0) cc_final: 0.9053 (t0) REVERT: H 66 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8743 (mtpp) REVERT: H 92 GLN cc_start: 0.9401 (pm20) cc_final: 0.8936 (pm20) REVERT: H 102 GLN cc_start: 0.9103 (mt0) cc_final: 0.8882 (pm20) REVERT: H 161 ASP cc_start: 0.9353 (OUTLIER) cc_final: 0.8905 (p0) REVERT: H 220 ASN cc_start: 0.9573 (m110) cc_final: 0.9370 (m-40) REVERT: z 16 ASP cc_start: 0.9577 (t0) cc_final: 0.9307 (t0) REVERT: K 16 ASP cc_start: 0.9398 (t0) cc_final: 0.8698 (t0) REVERT: K 18 ARG cc_start: 0.9423 (mtm110) cc_final: 0.8870 (tmt170) REVERT: P 16 ASP cc_start: 0.9567 (t0) cc_final: 0.9174 (t0) REVERT: S 16 ASP cc_start: 0.9362 (t0) cc_final: 0.9064 (t0) REVERT: Y 15 LEU cc_start: 0.9600 (tp) cc_final: 0.9276 (tm) REVERT: Y 16 ASP cc_start: 0.9518 (t0) cc_final: 0.9238 (t0) REVERT: b 42 THR cc_start: 0.9606 (p) cc_final: 0.9378 (t) REVERT: e 3 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7366 (pp20) REVERT: h 16 ASP cc_start: 0.9359 (t0) cc_final: 0.9013 (t0) REVERT: q 16 ASP cc_start: 0.9130 (t0) cc_final: 0.8803 (OUTLIER) REVERT: t 16 ASP cc_start: 0.9401 (t0) cc_final: 0.9132 (t70) REVERT: 3 16 ASP cc_start: 0.9344 (t0) cc_final: 0.9130 (OUTLIER) REVERT: 3 43 ASP cc_start: 0.9630 (m-30) cc_final: 0.9408 (m-30) REVERT: 6 16 ASP cc_start: 0.9275 (t0) cc_final: 0.8910 (t0) REVERT: 7 13 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7202 (tm-30) REVERT: d 34 THR cc_start: 0.9509 (OUTLIER) cc_final: 0.9275 (p) outliers start: 98 outliers final: 42 residues processed: 571 average time/residue: 0.8755 time to fit residues: 644.7413 Evaluate side-chains 518 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 470 time to evaluate : 3.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 205 LYS Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 180 HIS Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 218 PHE Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain Y residue 4 TYR Chi-restraints excluded: chain e residue 3 GLU Chi-restraints excluded: chain h residue 43 ASP Chi-restraints excluded: chain k residue 41 SER Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 13 GLU Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain f residue 2 ASP Chi-restraints excluded: chain i residue 13 GLU Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 47 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 13 GLU Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain j residue 21 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 190 optimal weight: 10.0000 chunk 122 optimal weight: 0.0010 chunk 183 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 241 optimal weight: 10.0000 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN L 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 33252 Z= 0.283 Angle : 0.933 18.774 46017 Z= 0.394 Chirality : 0.045 0.360 4813 Planarity : 0.005 0.083 5558 Dihedral : 16.371 179.967 5218 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.85 % Favored : 89.76 % Rotamer: Outliers : 2.77 % Allowed : 29.61 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3380 helix: 2.19 (0.12), residues: 1663 sheet: 0.24 (1.04), residues: 32 loop : -2.66 (0.16), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP m 30 HIS 0.008 0.001 HIS L 153 PHE 0.031 0.001 PHE 7 22 TYR 0.030 0.001 TYR V 27 ARG 0.020 0.001 ARG S 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 475 time to evaluate : 4.585 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: C 252 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8817 (p) REVERT: L 23 ASP cc_start: 0.9520 (t0) cc_final: 0.9083 (t0) REVERT: M 9 GLN cc_start: 0.9471 (mt0) cc_final: 0.9228 (mt0) REVERT: M 22 GLU cc_start: 0.9581 (tm-30) cc_final: 0.9276 (tm-30) REVERT: M 26 ASN cc_start: 0.9691 (OUTLIER) cc_final: 0.9476 (p0) REVERT: M 193 ASN cc_start: 0.9363 (t0) cc_final: 0.9079 (t0) REVERT: H 66 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8753 (mtpp) REVERT: H 92 GLN cc_start: 0.9457 (pm20) cc_final: 0.9094 (pm20) REVERT: H 102 GLN cc_start: 0.9090 (mt0) cc_final: 0.8872 (pm20) REVERT: H 161 ASP cc_start: 0.9360 (OUTLIER) cc_final: 0.8940 (p0) REVERT: z 16 ASP cc_start: 0.9556 (t0) cc_final: 0.9275 (t0) REVERT: K 16 ASP cc_start: 0.9379 (t0) cc_final: 0.9005 (t0) REVERT: P 16 ASP cc_start: 0.9529 (t0) cc_final: 0.9164 (t0) REVERT: S 16 ASP cc_start: 0.9343 (t0) cc_final: 0.9029 (t0) REVERT: Y 15 LEU cc_start: 0.9571 (tp) cc_final: 0.9251 (tm) REVERT: Y 16 ASP cc_start: 0.9501 (t0) cc_final: 0.9233 (t0) REVERT: b 42 THR cc_start: 0.9622 (p) cc_final: 0.9383 (t) REVERT: e 3 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7350 (pp20) REVERT: h 16 ASP cc_start: 0.9378 (t0) cc_final: 0.9019 (t0) REVERT: q 16 ASP cc_start: 0.9103 (t0) cc_final: 0.8750 (OUTLIER) REVERT: t 16 ASP cc_start: 0.9360 (t0) cc_final: 0.9092 (t70) REVERT: 3 16 ASP cc_start: 0.9398 (t0) cc_final: 0.9179 (t0) REVERT: 3 43 ASP cc_start: 0.9639 (m-30) cc_final: 0.9421 (m-30) REVERT: 6 16 ASP cc_start: 0.9337 (t0) cc_final: 0.8993 (t0) REVERT: 4 13 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: 4 36 VAL cc_start: 0.9641 (t) cc_final: 0.9434 (p) outliers start: 81 outliers final: 53 residues processed: 529 average time/residue: 0.8883 time to fit residues: 605.1576 Evaluate side-chains 522 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 464 time to evaluate : 3.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 205 LYS Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 180 HIS Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 218 PHE Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain Y residue 4 TYR Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain e residue 3 GLU Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain k residue 41 SER Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain i residue 13 GLU Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 13 GLU Chi-restraints excluded: chain 4 residue 47 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 13 GLU Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 23 ILE Chi-restraints excluded: chain j residue 21 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 279 optimal weight: 50.0000 chunk 294 optimal weight: 4.9990 chunk 268 optimal weight: 6.9990 chunk 286 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 224 optimal weight: 0.3980 chunk 87 optimal weight: 0.0060 chunk 258 optimal weight: 0.7980 chunk 270 optimal weight: 0.9990 chunk 285 optimal weight: 1.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 257 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 33252 Z= 0.226 Angle : 0.918 19.728 46017 Z= 0.390 Chirality : 0.045 0.292 4813 Planarity : 0.004 0.069 5558 Dihedral : 16.087 179.364 5218 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.17 % Favored : 90.50 % Rotamer: Outliers : 2.02 % Allowed : 30.43 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 3380 helix: 2.11 (0.12), residues: 1662 sheet: 0.23 (1.03), residues: 32 loop : -2.59 (0.16), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP m 30 HIS 0.004 0.001 HIS L 153 PHE 0.030 0.001 PHE n 25 TYR 0.031 0.001 TYR V 27 ARG 0.016 0.001 ARG z 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 518 time to evaluate : 3.267 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: C 110 MET cc_start: 0.9335 (mmt) cc_final: 0.8733 (mmt) REVERT: C 233 MET cc_start: 0.9133 (mmp) cc_final: 0.8467 (mmt) REVERT: C 252 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8810 (p) REVERT: L 23 ASP cc_start: 0.9492 (t0) cc_final: 0.9073 (t0) REVERT: L 29 TYR cc_start: 0.9301 (m-80) cc_final: 0.9052 (m-80) REVERT: M 9 GLN cc_start: 0.9474 (mt0) cc_final: 0.9203 (mt0) REVERT: M 22 GLU cc_start: 0.9584 (tm-30) cc_final: 0.9257 (tm-30) REVERT: M 26 ASN cc_start: 0.9691 (OUTLIER) cc_final: 0.9483 (p0) REVERT: M 193 ASN cc_start: 0.9320 (t0) cc_final: 0.9052 (t0) REVERT: H 66 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8783 (mtpp) REVERT: H 92 GLN cc_start: 0.9458 (pm20) cc_final: 0.9101 (pm20) REVERT: H 161 ASP cc_start: 0.9391 (OUTLIER) cc_final: 0.8952 (p0) REVERT: H 217 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8806 (pm20) REVERT: z 16 ASP cc_start: 0.9525 (t0) cc_final: 0.9267 (t0) REVERT: K 16 ASP cc_start: 0.9348 (t0) cc_final: 0.8985 (t0) REVERT: K 29 THR cc_start: 0.9450 (m) cc_final: 0.9105 (p) REVERT: K 43 ASP cc_start: 0.9404 (m-30) cc_final: 0.9117 (t0) REVERT: P 16 ASP cc_start: 0.9457 (t0) cc_final: 0.9090 (t0) REVERT: S 16 ASP cc_start: 0.9339 (t0) cc_final: 0.9033 (t0) REVERT: Y 16 ASP cc_start: 0.9481 (t0) cc_final: 0.9215 (t0) REVERT: b 42 THR cc_start: 0.9595 (p) cc_final: 0.9288 (t) REVERT: h 16 ASP cc_start: 0.9347 (t0) cc_final: 0.8970 (t0) REVERT: q 16 ASP cc_start: 0.9041 (t0) cc_final: 0.8678 (OUTLIER) REVERT: t 16 ASP cc_start: 0.9390 (t0) cc_final: 0.9104 (t70) REVERT: 3 43 ASP cc_start: 0.9591 (m-30) cc_final: 0.9384 (m-30) REVERT: 6 16 ASP cc_start: 0.9281 (t0) cc_final: 0.8938 (t0) REVERT: u 36 VAL cc_start: 0.9509 (t) cc_final: 0.9251 (p) REVERT: 4 36 VAL cc_start: 0.9621 (t) cc_final: 0.9417 (p) REVERT: 7 14 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8658 (pp20) REVERT: d 34 THR cc_start: 0.9397 (t) cc_final: 0.9158 (p) REVERT: s 17 LEU cc_start: 0.7708 (mt) cc_final: 0.7238 (mt) outliers start: 59 outliers final: 39 residues processed: 561 average time/residue: 0.8738 time to fit residues: 636.1068 Evaluate side-chains 525 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 481 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 205 LYS Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 180 HIS Chi-restraints excluded: chain M residue 210 CYS Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain H residue 218 PHE Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain b residue 14 ILE Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain t residue 15 LEU Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain f residue 2 ASP Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 30 LEU Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 14 GLU Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain a residue 21 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 188 optimal weight: 0.7980 chunk 302 optimal weight: 0.8980 chunk 184 optimal weight: 30.0000 chunk 143 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 317 optimal weight: 0.0870 chunk 292 optimal weight: 1.9990 chunk 253 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 33252 Z= 0.233 Angle : 0.932 18.693 46017 Z= 0.397 Chirality : 0.045 0.271 4813 Planarity : 0.005 0.150 5558 Dihedral : 15.976 179.746 5218 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.23 % Favored : 90.44 % Rotamer: Outliers : 1.74 % Allowed : 31.15 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3380 helix: 2.06 (0.12), residues: 1659 sheet: 0.22 (1.02), residues: 32 loop : -2.55 (0.16), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP j 30 HIS 0.006 0.001 HIS L 153 PHE 0.035 0.001 PHE 7 22 TYR 0.031 0.001 TYR V 27 ARG 0.023 0.001 ARG S 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 502 time to evaluate : 3.686 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: C 233 MET cc_start: 0.9143 (mmp) cc_final: 0.8475 (mmt) REVERT: L 23 ASP cc_start: 0.9492 (t0) cc_final: 0.9087 (t0) REVERT: L 29 TYR cc_start: 0.9295 (m-80) cc_final: 0.8992 (m-80) REVERT: M 9 GLN cc_start: 0.9486 (mt0) cc_final: 0.9210 (mt0) REVERT: M 22 GLU cc_start: 0.9599 (tm-30) cc_final: 0.9294 (tm-30) REVERT: M 26 ASN cc_start: 0.9668 (OUTLIER) cc_final: 0.9450 (p0) REVERT: M 193 ASN cc_start: 0.9312 (t0) cc_final: 0.9042 (t0) REVERT: H 92 GLN cc_start: 0.9347 (pm20) cc_final: 0.9131 (pm20) REVERT: H 161 ASP cc_start: 0.9378 (OUTLIER) cc_final: 0.8869 (p0) REVERT: H 217 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8823 (pm20) REVERT: z 16 ASP cc_start: 0.9518 (t0) cc_final: 0.9215 (t0) REVERT: K 16 ASP cc_start: 0.9329 (t0) cc_final: 0.8965 (t0) REVERT: K 43 ASP cc_start: 0.9404 (m-30) cc_final: 0.9132 (t0) REVERT: P 16 ASP cc_start: 0.9422 (t0) cc_final: 0.9036 (t0) REVERT: S 16 ASP cc_start: 0.9325 (t0) cc_final: 0.9015 (t0) REVERT: Y 16 ASP cc_start: 0.9464 (t0) cc_final: 0.9214 (t0) REVERT: b 42 THR cc_start: 0.9592 (p) cc_final: 0.9280 (t) REVERT: e 16 ASP cc_start: 0.9241 (t0) cc_final: 0.9037 (t0) REVERT: h 16 ASP cc_start: 0.9321 (t0) cc_final: 0.8943 (t0) REVERT: k 54 LEU cc_start: 0.9456 (mm) cc_final: 0.9194 (pt) REVERT: q 16 ASP cc_start: 0.8990 (t0) cc_final: 0.8622 (OUTLIER) REVERT: t 16 ASP cc_start: 0.9343 (t0) cc_final: 0.9023 (t70) REVERT: 3 16 ASP cc_start: 0.9252 (t0) cc_final: 0.8914 (t0) REVERT: 3 19 ARG cc_start: 0.8953 (mtp85) cc_final: 0.8660 (pmm-80) REVERT: 3 43 ASP cc_start: 0.9584 (m-30) cc_final: 0.9379 (m-30) REVERT: 6 16 ASP cc_start: 0.9255 (t0) cc_final: 0.8903 (t0) REVERT: i 13 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: u 36 VAL cc_start: 0.9537 (t) cc_final: 0.9314 (p) REVERT: d 34 THR cc_start: 0.9391 (t) cc_final: 0.9159 (p) REVERT: j 33 LEU cc_start: 0.9689 (mm) cc_final: 0.9327 (mm) REVERT: s 17 LEU cc_start: 0.7523 (mt) cc_final: 0.7094 (mt) outliers start: 51 outliers final: 40 residues processed: 536 average time/residue: 0.8349 time to fit residues: 584.9577 Evaluate side-chains 520 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 477 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 205 LYS Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 180 HIS Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain H residue 218 PHE Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain Y residue 4 TYR Chi-restraints excluded: chain b residue 14 ILE Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain k residue 41 SER Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain t residue 15 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain i residue 13 GLU Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 30 LEU Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain p residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 201 optimal weight: 6.9990 chunk 269 optimal weight: 0.1980 chunk 77 optimal weight: 2.9990 chunk 233 optimal weight: 0.1980 chunk 37 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 253 optimal weight: 0.9990 chunk 106 optimal weight: 0.0470 chunk 260 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.066686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.049067 restraints weight = 111037.964| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 4.25 r_work: 0.2679 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 33252 Z= 0.227 Angle : 0.927 18.632 46017 Z= 0.397 Chirality : 0.045 0.337 4813 Planarity : 0.005 0.163 5558 Dihedral : 15.852 179.013 5216 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.61 % Favored : 91.12 % Rotamer: Outliers : 1.54 % Allowed : 31.80 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3380 helix: 2.02 (0.12), residues: 1653 sheet: 0.19 (1.02), residues: 32 loop : -2.51 (0.16), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP m 30 HIS 0.005 0.001 HIS L 153 PHE 0.030 0.001 PHE n 25 TYR 0.032 0.001 TYR V 27 ARG 0.025 0.001 ARG b 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11079.92 seconds wall clock time: 196 minutes 44.32 seconds (11804.32 seconds total)