Starting phenix.real_space_refine on Sat Feb 17 16:49:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dcq_7858/02_2024/6dcq_7858_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dcq_7858/02_2024/6dcq_7858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dcq_7858/02_2024/6dcq_7858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dcq_7858/02_2024/6dcq_7858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dcq_7858/02_2024/6dcq_7858_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dcq_7858/02_2024/6dcq_7858_updated.pdb" } resolution = 3.1 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= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 12064 2.51 5 N 3154 2.21 5 O 3972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 293": "NH1" <-> "NH2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C ARG 350": "NH1" <-> "NH2" Residue "C ARG 429": "NH1" <-> "NH2" Residue "C ARG 444": "NH1" <-> "NH2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E ARG 429": "NH1" <-> "NH2" Residue "E ARG 444": "NH1" <-> "NH2" Residue "E ARG 444": "NH1" <-> "NH2" Residue "E ARG 504": "NH1" <-> "NH2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19300 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 3413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 435, 3403 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 435, 3403 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 5 bond proxies already assigned to first conformer: 3458 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 3553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3538 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 23, 'TRANS': 428} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 452, 3538 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 23, 'TRANS': 428} Chain breaks: 4 bond proxies already assigned to first conformer: 3592 Chain: "D" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1167 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 1, 'TRANS': 144} Chain: "E" Number of atoms: 3536 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 448, 3515 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 23, 'TRANS': 424} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 448, 3515 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 23, 'TRANS': 424} Chain breaks: 4 bond proxies already assigned to first conformer: 3563 Chain: "F" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1095 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 1, 'TRANS': 137} Chain breaks: 1 Chain: "H" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1050 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "L" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 846 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "M" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1067 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "N" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "g" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 113 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 113 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "s" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 110 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 1, 'NAG': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AHIS A 173 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 173 " occ=0.50 residue: pdb=" N AHIS E 173 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS E 173 " occ=0.50 residue: pdb=" N AARG E 444 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 444 " occ=0.50 Time building chain proxies: 15.16, per 1000 atoms: 0.79 Number of scatterers: 19300 At special positions: 0 Unit cell: (152.44, 133.9, 128.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 3972 8.00 N 3154 7.00 C 12064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.23 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 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=5, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN k 4 " - " MAN k 5 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA c 3 " - " MAN c 4 " " BMA f 3 " - " MAN f 9 " " BMA g 3 " - " MAN g 4 " " BMA k 3 " - " MAN k 4 " " MAN k 6 " - " MAN k 7 " " BMA r 3 " - " MAN r 4 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " BMA c 3 " - " MAN c 5 " " BMA f 3 " - " MAN f 4 " " BMA g 3 " - " MAN g 7 " " BMA k 3 " - " MAN k 6 " " BMA r 3 " - " MAN r 7 " " BMA s 3 " - " MAN s 4 " BETA1-2 " MAN f 4 " - " NAG f 5 " " MAN g 4 " - " NAG g 5 " " MAN g 7 " - " NAG g 8 " " MAN r 4 " - " NAG r 5 " " MAN r 7 " - " NAG r 8 " " MAN s 4 " - " NAG s 5 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG f 5 " - " GAL f 6 " " NAG f 7 " - " GAL f 8 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " MAN g 4 " - " NAG g 6 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " MAN r 4 " - " NAG r 6 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG s 5 " - " GAL s 6 " " NAG s 7 " - " GAL s 8 " BETA1-6 " NAG G 1 " - " FUC G 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG V 1 " - " FUC V 3 " " NAG f 1 " - " FUC f 10 " " MAN f 4 " - " NAG f 7 " " NAG g 1 " - " FUC g 9 " " NAG r 1 " - " FUC r 9 " " NAG s 1 " - " FUC s 9 " " MAN s 4 " - " NAG s 7 " NAG-ASN " NAG A 607 " - " ASN A 448 " " NAG A 612 " - " ASN A 234 " " NAG A 617 " - " ASN A 356 " " NAG A 628 " - " ASN A 301 " " NAG B1000 " - " ASN B 616 " " NAG B1003 " - " ASN B 637 " " NAG B1004 " - " ASN B 625 " " NAG C 601 " - " ASN C 356 " " NAG C 611 " - " ASN C 392 " " NAG C 612 " - " ASN C 276 " " NAG C 613 " - " ASN C 234 " " NAG C 614 " - " ASN C 88 " " NAG D1019 " - " ASN D 616 " " NAG D1020 " - " ASN D 625 " " NAG E 618 " - " ASN E 356 " " NAG E 619 " - " ASN E 88 " " NAG E 620 " - " ASN E 392 " " NAG E 623 " - " ASN E 234 " " NAG E 630 " - " ASN E 197 " " NAG F 901 " - " ASN F 625 " " NAG F 902 " - " ASN F 616 " " NAG G 1 " - " ASN A 197 " " NAG I 1 " - " ASN A 332 " " NAG J 1 " - " ASN A 295 " " NAG K 1 " - " ASN A 130 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 88 " " NAG R 1 " - " ASN A 392 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN B 611 " " NAG V 1 " - " ASN C 197 " " NAG W 1 " - " ASN C 160 " " NAG X 1 " - " ASN C 130 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 332 " " NAG a 1 " - " ASN C 295 " " NAG b 1 " - " ASN C 448 " " NAG c 1 " - " ASN C 262 " " NAG d 1 " - " ASN C 301 " " NAG e 1 " - " ASN C 386 " " NAG f 1 " - " ASN D 611 " " NAG g 1 " - " ASN D 637 " " NAG h 1 " - " ASN E 295 " " NAG i 1 " - " ASN E 301 " " NAG j 1 " - " ASN E 156 " " NAG k 1 " - " ASN E 262 " " NAG l 1 " - " ASN E 448 " " NAG m 1 " - " ASN E 332 " " NAG n 1 " - " ASN E 386 " " NAG o 1 " - " ASN E 276 " " NAG p 1 " - " ASN E 160 " " NAG r 1 " - " ASN F 637 " " NAG s 1 " - " ASN F 611 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.90 Conformation dependent library (CDL) restraints added in 4.7 seconds 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 33 sheets defined 15.2% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.12 Creating SS restraints... Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.604A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.573A pdb=" N GLU A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.865A pdb=" N ARG A 480 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 537 through 541 removed outlier: 3.551A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 537 through 541' Processing helix chain 'B' and resid 574 through 595 removed outlier: 3.626A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 623 No H-bonds generated for 'chain 'B' and resid 620 through 623' Processing helix chain 'B' and resid 628 through 634 removed outlier: 3.812A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 651 removed outlier: 3.700A pdb=" N GLN B 650 " --> pdb=" O ILE B 646 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 112 removed outlier: 3.859A pdb=" N ASP C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 337 through 353 removed outlier: 3.575A pdb=" N ALA C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 475 through 480 removed outlier: 3.636A pdb=" N ARG C 480 " --> pdb=" O ASN C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.567A pdb=" N ALA D 541 " --> pdb=" O THR D 538 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG D 542 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 564 Processing helix chain 'D' and resid 570 through 590 removed outlier: 3.778A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 582 " --> pdb=" O ALA D 578 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 595 No H-bonds generated for 'chain 'D' and resid 592 through 595' Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 632 through 635 No H-bonds generated for 'chain 'D' and resid 632 through 635' Processing helix chain 'D' and resid 639 through 659 removed outlier: 3.635A pdb=" N TYR D 644 " --> pdb=" O ASP D 640 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 645 " --> pdb=" O THR D 641 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP D 659 " --> pdb=" O VAL D 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 100 through 117 removed outlier: 3.745A pdb=" N SER E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 335 through 349 Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 476 through 480 Processing helix chain 'F' and resid 537 through 541 Processing helix chain 'F' and resid 570 through 595 removed outlier: 3.708A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR F 586 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY F 594 " --> pdb=" O GLN F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 622 No H-bonds generated for 'chain 'F' and resid 619 through 622' Processing helix chain 'F' and resid 632 through 635 No H-bonds generated for 'chain 'F' and resid 632 through 635' Processing helix chain 'F' and resid 639 through 659 removed outlier: 3.581A pdb=" N LEU F 645 " --> pdb=" O THR F 641 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.565A pdb=" N ALA A 497 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.413A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 189 through 191 Processing sheet with id= D, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.377A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 413 through 417 removed outlier: 4.274A pdb=" N SER A 334 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.619A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 303 through 308 removed outlier: 3.836A pdb=" N ASP A 322 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N THR A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR A 320 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 36 through 40 Processing sheet with id= I, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.709A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 91 through 93 Processing sheet with id= K, first strand: chain 'C' and resid 130 through 132 Processing sheet with id= L, first strand: chain 'C' and resid 159 through 161 Processing sheet with id= M, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.519A pdb=" N THR C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE C 468 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 443 through 449 removed outlier: 3.739A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER C 334 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.380A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 302 through 309 removed outlier: 3.781A pdb=" N ASP C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N THR C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N THR C 320 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE C 309 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= R, first strand: chain 'E' and resid 83 through 85 removed outlier: 3.980A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 129 through 131 removed outlier: 3.514A pdb=" N CYS E 131 " --> pdb=" O SER E 189 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 154 through 162 Processing sheet with id= U, first strand: chain 'E' and resid 271 through 273 Processing sheet with id= V, first strand: chain 'E' and resid 443 through 449 removed outlier: 4.009A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG E 298 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ARG E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER E 334 " --> pdb=" O ARG E 293 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 305 through 308 Processing sheet with id= X, first strand: chain 'E' and resid 358 through 360 Processing sheet with id= Y, first strand: chain 'H' and resid 37 through 39 removed outlier: 3.647A pdb=" N VAL H 37 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 70 through 72 Processing sheet with id= AA, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= AB, first strand: chain 'L' and resid 35 through 38 removed outlier: 3.511A pdb=" N TRP L 35 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU L 46 " --> pdb=" O ARG L 37 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'M' and resid 3 through 7 removed outlier: 4.470A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL M 18 " --> pdb=" O MET M 82 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET M 82 " --> pdb=" O VAL M 18 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU M 80 " --> pdb=" O LEU M 20 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 107 through 109 removed outlier: 3.515A pdb=" N ALA M 93 " --> pdb=" O TYR M 35 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ALA M 40 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU M 45 " --> pdb=" O ALA M 40 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'M' and resid 100C through 100E removed outlier: 3.513A pdb=" N ARG M 100J" --> pdb=" O ASP M 100E" (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.723A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR N 72 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER N 65 " --> pdb=" O THR N 72 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL N 63 " --> pdb=" O ARG N 74 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.605A pdb=" N LYS N 103 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR N 86 " --> pdb=" O THR N 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU N 46 " --> pdb=" O ARG N 37 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1104 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: 5.55 Time building geometry restraints manager: 10.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5900 1.34 - 1.47: 5255 1.47 - 1.60: 8366 1.60 - 1.73: 0 1.73 - 1.86: 149 Bond restraints: 19670 Sorted by residual: bond pdb=" C VAL E 411 " pdb=" N PRO E 411B" ideal model delta sigma weight residual 1.334 1.391 -0.058 8.40e-03 1.42e+04 4.73e+01 bond pdb=" C PHE C 468 " pdb=" N ARG C 469 " ideal model delta sigma weight residual 1.333 1.249 0.083 2.74e-02 1.33e+03 9.26e+00 bond pdb=" CA ASN E 295 " pdb=" CB ASN E 295 " ideal model delta sigma weight residual 1.533 1.598 -0.065 2.29e-02 1.91e+03 7.96e+00 bond pdb=" C1 NAG E 620 " pdb=" O5 NAG E 620 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.04e+00 bond pdb=" C5 MAN S 4 " pdb=" O5 MAN S 4 " ideal model delta sigma weight residual 1.418 1.471 -0.053 2.00e-02 2.50e+03 6.93e+00 ... (remaining 19665 not shown) Histogram of bond angle deviations from ideal: 95.70 - 103.40: 214 103.40 - 111.10: 8293 111.10 - 118.81: 8116 118.81 - 126.51: 9711 126.51 - 134.21: 360 Bond angle restraints: 26694 Sorted by residual: angle pdb=" C ASN E 295 " pdb=" CA ASN E 295 " pdb=" CB ASN E 295 " ideal model delta sigma weight residual 109.37 117.92 -8.55 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C THR H 107 " pdb=" N THR H 108 " pdb=" CA THR H 108 " ideal model delta sigma weight residual 122.82 129.08 -6.26 1.42e+00 4.96e-01 1.94e+01 angle pdb=" C LYS A 269 " pdb=" N VAL A 270 " pdb=" CA VAL A 270 " ideal model delta sigma weight residual 121.97 129.91 -7.94 1.80e+00 3.09e-01 1.94e+01 angle pdb=" C TRP F 628 " pdb=" N LEU F 629 " pdb=" CA LEU F 629 " ideal model delta sigma weight residual 121.54 129.75 -8.21 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C VAL E 505 " pdb=" N VAL E 506 " pdb=" CA VAL E 506 " ideal model delta sigma weight residual 121.70 129.12 -7.42 1.80e+00 3.09e-01 1.70e+01 ... (remaining 26689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.39: 12966 23.39 - 46.78: 385 46.78 - 70.16: 84 70.16 - 93.55: 47 93.55 - 116.94: 27 Dihedral angle restraints: 13509 sinusoidal: 7072 harmonic: 6437 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -161.26 75.26 1 1.00e+01 1.00e-02 7.16e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 154.59 -61.59 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS E 131 " pdb=" SG CYS E 131 " pdb=" SG CYS E 157 " pdb=" CB CYS E 157 " ideal model delta sinusoidal sigma weight residual 93.00 37.87 55.13 1 1.00e+01 1.00e-02 4.11e+01 ... (remaining 13506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 3349 0.197 - 0.394: 37 0.394 - 0.591: 7 0.591 - 0.789: 0 0.789 - 0.986: 1 Chirality restraints: 3394 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 332 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 130 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 386 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.33e+00 ... (remaining 3391 not shown) Planarity restraints: 3258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 479 " -0.022 2.00e-02 2.50e+03 2.12e-02 1.12e+01 pdb=" CG TRP E 479 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP E 479 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP E 479 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 479 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP E 479 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 479 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 479 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 479 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 479 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 356 " -0.031 2.00e-02 2.50e+03 2.97e-02 1.11e+01 pdb=" CG ASN E 356 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN E 356 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN E 356 " 0.029 2.00e-02 2.50e+03 pdb=" C1 NAG E 618 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 93 " -0.025 2.00e-02 2.50e+03 2.48e-02 1.08e+01 pdb=" CG PHE A 93 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE A 93 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 93 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 93 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 93 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 93 " -0.004 2.00e-02 2.50e+03 ... (remaining 3255 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 49 2.43 - 3.05: 11350 3.05 - 3.67: 26086 3.67 - 4.28: 40958 4.28 - 4.90: 67142 Nonbonded interactions: 145585 Sorted by model distance: nonbonded pdb=" OE1 GLU C 335 " pdb=" C ASN C 411C" model vdw 1.817 3.270 nonbonded pdb=" OE1 GLU C 335 " pdb=" CB ASN C 411C" model vdw 1.855 3.440 nonbonded pdb=" OE1 GLU C 335 " pdb=" CA ASN C 411C" model vdw 1.964 3.470 nonbonded pdb=" OE1 GLU C 335 " pdb=" O ASN C 411C" model vdw 1.989 3.040 nonbonded pdb=" ND2 ASN E 130 " pdb=" O5 NAG q 1 " model vdw 2.072 2.520 ... (remaining 145580 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 'A' and (resid 32 through 165 or resid 167 through 172 or resid 174 throu \ gh 185 or resid 188 through 443 or resid 445 through 457 or resid 464 through 50 \ 6 or resid 607 through 628)) selection = (chain 'C' and (resid 32 through 58 or resid 71 through 136 or resid 147 through \ 165 or resid 167 through 172 or resid 174 through 398 or resid 411 through 443 \ or resid 445 through 457 or resid 464 through 506 or resid 611 through 614)) selection = (chain 'E' and (resid 32 through 58 or resid 71 through 136 or resid 147 through \ 165 or resid 167 through 172 or resid 174 through 185 or resid 188 through 443 \ or resid 445 through 457 or resid 464 through 506 or resid 619 through 630)) } ncs_group { reference = (chain 'B' and (resid 512 through 655 or resid 1003 through 1004)) selection = (chain 'F' and (resid 512 through 549 or resid 572 through 655 or resid 901 thro \ ugh 902)) } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'i' and resid 1) selection = (chain 'j' and resid 1) selection = (chain 'l' and resid 1) selection = (chain 'm' and resid 1) selection = (chain 'n' and resid 1) selection = (chain 'o' and resid 1) selection = (chain 'p' and resid 1) selection = (chain 'q' and resid 1) } ncs_group { reference = chain 'H' selection = (chain 'M' and resid 2 through 111) } ncs_group { reference = (chain 'L' and resid 2 through 105) selection = (chain 'N' and resid 2 through 105) } ncs_group { reference = (chain 'S' and (resid 1 or resid 4 through 6)) selection = (chain 'k' and (resid 2 or resid 5 through 7)) } ncs_group { reference = (chain 'f' and (resid 2 or resid 10)) selection = (chain 'g' and (resid 1 or resid 9)) selection = (chain 'r' and (resid 1 or resid 9)) selection = (chain 's' and (resid 1 or resid 9)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 8.070 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 60.730 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.180 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: 0.000 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 : 0.008 0.085 19670 Z= 0.507 Angle : 1.073 10.115 26694 Z= 0.536 Chirality : 0.071 0.986 3394 Planarity : 0.007 0.069 3203 Dihedral : 13.004 116.940 9259 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.34 % Favored : 91.56 % Rotamer: Outliers : 0.36 % Allowed : 1.99 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -4.41 (0.14), residues: 2192 helix: -4.37 (0.11), residues: 364 sheet: -2.55 (0.19), residues: 573 loop : -2.69 (0.14), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.005 TRP E 479 HIS 0.013 0.002 HIS A 374 PHE 0.057 0.005 PHE A 93 TYR 0.038 0.003 TYR C 191 ARG 0.011 0.001 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 467 time to evaluate : 2.097 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: A 368 ASP cc_start: 0.7290 (t0) cc_final: 0.7030 (t70) REVERT: B 513 VAL cc_start: 0.9002 (t) cc_final: 0.8732 (m) REVERT: B 639 THR cc_start: 0.9013 (m) cc_final: 0.8808 (p) REVERT: C 426 MET cc_start: 0.8357 (tpt) cc_final: 0.8124 (tpt) REVERT: D 657 GLU cc_start: 0.8116 (pp20) cc_final: 0.7883 (pp20) REVERT: E 330 TYR cc_start: 0.8645 (p90) cc_final: 0.8415 (p90) REVERT: F 633 LYS cc_start: 0.8781 (mttt) cc_final: 0.8530 (mptt) REVERT: H 23 VAL cc_start: 0.7240 (t) cc_final: 0.6962 (m) REVERT: L 4 MET cc_start: 0.7686 (mmm) cc_final: 0.7355 (mmp) REVERT: L 92 LYS cc_start: 0.8873 (tmtm) cc_final: 0.8608 (tttm) REVERT: M 13 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7308 (mp10) REVERT: M 53 ASP cc_start: 0.7878 (t0) cc_final: 0.7599 (t0) REVERT: N 75 ILE cc_start: 0.8464 (mt) cc_final: 0.8143 (mt) REVERT: N 83 VAL cc_start: 0.8970 (m) cc_final: 0.8656 (t) outliers start: 5 outliers final: 0 residues processed: 470 average time/residue: 0.3551 time to fit residues: 239.6997 Evaluate side-chains 276 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 8.9990 chunk 165 optimal weight: 0.7980 chunk 92 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 104 optimal weight: 0.2980 chunk 127 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 276 ASN A 352 HIS A 411CASN A 425 ASN A 478 ASN B 619 GLN C 72 HIS C 103 GLN C 146 ASN C 216 HIS ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 552 GLN D 607 ASN D 656 ASN E 32 ASN E 82 GLN E 103 GLN E 187 ASN E 195 ASN ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN E 348 GLN E 432 GLN E 478 ASN F 575 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN N 6 GLN N 27DGLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 19670 Z= 0.205 Angle : 0.703 14.977 26694 Z= 0.351 Chirality : 0.050 0.475 3394 Planarity : 0.005 0.060 3203 Dihedral : 11.740 87.807 5115 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.38 % Allowed : 8.27 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.05 % 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: -3.28 (0.15), residues: 2192 helix: -2.33 (0.21), residues: 357 sheet: -1.96 (0.20), residues: 576 loop : -2.26 (0.15), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 479 HIS 0.003 0.001 HIS E 105 PHE 0.027 0.002 PHE L 49 TYR 0.021 0.001 TYR C 61 ARG 0.006 0.001 ARG L 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 320 time to evaluate : 2.089 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: B 513 VAL cc_start: 0.8994 (t) cc_final: 0.8767 (m) REVERT: B 621 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7356 (tm-30) REVERT: B 626 MET cc_start: 0.8041 (tpp) cc_final: 0.7824 (ttt) REVERT: C 102 GLU cc_start: 0.7330 (tp30) cc_final: 0.7111 (mm-30) REVERT: C 378 CYS cc_start: 0.5787 (t) cc_final: 0.5301 (t) REVERT: C 426 MET cc_start: 0.8292 (tpt) cc_final: 0.7941 (tpt) REVERT: E 133 ASN cc_start: 0.8196 (p0) cc_final: 0.7974 (m-40) REVERT: F 545 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8965 (tp) REVERT: L 35 TRP cc_start: 0.7054 (m100) cc_final: 0.6611 (m100) REVERT: M 13 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7450 (mp10) REVERT: M 53 ASP cc_start: 0.7811 (t0) cc_final: 0.7495 (t0) REVERT: N 24 LYS cc_start: 0.8112 (tptt) cc_final: 0.7440 (mtmm) REVERT: N 39 LYS cc_start: 0.7533 (mmtt) cc_final: 0.7179 (mmtt) outliers start: 25 outliers final: 18 residues processed: 331 average time/residue: 0.3468 time to fit residues: 168.7394 Evaluate side-chains 286 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 267 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 30 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN C 72 HIS C 374 HIS E 32 ASN E 82 GLN E 374 HIS F 540 GLN F 577 GLN F 651 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 19670 Z= 0.439 Angle : 0.809 13.990 26694 Z= 0.398 Chirality : 0.054 0.529 3394 Planarity : 0.006 0.084 3203 Dihedral : 11.188 82.997 5115 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.01 % Allowed : 8.98 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.09 % 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: -2.80 (0.16), residues: 2192 helix: -1.28 (0.25), residues: 362 sheet: -1.81 (0.20), residues: 569 loop : -2.09 (0.15), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 45 HIS 0.008 0.002 HIS H 56 PHE 0.035 0.003 PHE A 93 TYR 0.028 0.002 TYR C 191 ARG 0.008 0.001 ARG A 480 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 263 time to evaluate : 2.089 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: B 621 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7479 (tm-30) REVERT: C 102 GLU cc_start: 0.7447 (tp30) cc_final: 0.7228 (mm-30) REVERT: C 378 CYS cc_start: 0.6264 (t) cc_final: 0.5906 (t) REVERT: C 426 MET cc_start: 0.8425 (tpt) cc_final: 0.8130 (tpt) REVERT: E 486 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.6746 (p90) REVERT: F 545 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9086 (tm) REVERT: F 567 ARG cc_start: 0.6132 (ptm160) cc_final: 0.5858 (ptp-110) REVERT: L 103 LYS cc_start: 0.6602 (mmtt) cc_final: 0.6378 (mmmt) REVERT: M 13 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7489 (mp10) REVERT: M 53 ASP cc_start: 0.8011 (t0) cc_final: 0.7811 (t0) REVERT: N 24 LYS cc_start: 0.8183 (tptt) cc_final: 0.7462 (mtmm) REVERT: N 61 ARG cc_start: 0.6541 (mtm180) cc_final: 0.6277 (ptp90) REVERT: N 82 ASP cc_start: 0.7137 (m-30) cc_final: 0.6054 (m-30) outliers start: 57 outliers final: 42 residues processed: 295 average time/residue: 0.3376 time to fit residues: 148.5255 Evaluate side-chains 290 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 246 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 196 optimal weight: 0.1980 chunk 149 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 133 optimal weight: 6.9990 chunk 199 optimal weight: 0.9980 chunk 211 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS E 82 GLN F 577 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19670 Z= 0.198 Angle : 0.657 13.288 26694 Z= 0.320 Chirality : 0.049 0.432 3394 Planarity : 0.004 0.056 3203 Dihedral : 10.031 70.633 5115 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.84 % Allowed : 11.17 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.36 (0.16), residues: 2192 helix: -0.54 (0.27), residues: 350 sheet: -1.60 (0.20), residues: 593 loop : -1.87 (0.16), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 338 HIS 0.004 0.001 HIS E 105 PHE 0.024 0.002 PHE N 49 TYR 0.020 0.001 TYR C 191 ARG 0.013 0.000 ARG N 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 276 time to evaluate : 2.137 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: B 621 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7574 (tm-30) REVERT: C 378 CYS cc_start: 0.6141 (t) cc_final: 0.5780 (t) REVERT: F 545 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8956 (tp) REVERT: F 567 ARG cc_start: 0.6103 (ptm160) cc_final: 0.5833 (ptp-110) REVERT: H 64 GLN cc_start: 0.8186 (tp-100) cc_final: 0.7981 (tp-100) REVERT: L 75 ILE cc_start: 0.6201 (mm) cc_final: 0.5822 (mt) REVERT: L 103 LYS cc_start: 0.6636 (mmtt) cc_final: 0.6429 (mmmm) REVERT: M 13 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7326 (mp10) REVERT: M 53 ASP cc_start: 0.7852 (t0) cc_final: 0.7538 (t0) REVERT: N 24 LYS cc_start: 0.8279 (tptt) cc_final: 0.7577 (mtmm) outliers start: 34 outliers final: 22 residues processed: 295 average time/residue: 0.3266 time to fit residues: 145.1014 Evaluate side-chains 272 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 249 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain M residue 111 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 53 optimal weight: 0.0770 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS F 651 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19670 Z= 0.232 Angle : 0.657 12.878 26694 Z= 0.317 Chirality : 0.049 0.433 3394 Planarity : 0.004 0.050 3203 Dihedral : 9.474 68.569 5115 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.40 % Allowed : 11.58 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.10 (0.17), residues: 2192 helix: -0.21 (0.28), residues: 355 sheet: -1.42 (0.20), residues: 593 loop : -1.75 (0.16), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 338 HIS 0.004 0.001 HIS C 374 PHE 0.027 0.002 PHE H 67 TYR 0.021 0.001 TYR C 191 ARG 0.004 0.000 ARG N 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 263 time to evaluate : 2.155 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: B 621 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7588 (tm-30) REVERT: C 378 CYS cc_start: 0.6175 (t) cc_final: 0.5834 (t) REVERT: E 191 TYR cc_start: 0.8484 (m-80) cc_final: 0.8182 (m-80) REVERT: E 486 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.7088 (p90) REVERT: F 545 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8962 (tp) REVERT: F 567 ARG cc_start: 0.6232 (ptm160) cc_final: 0.5865 (ptp-110) REVERT: H 81 GLU cc_start: 0.7349 (tp30) cc_final: 0.7006 (mm-30) REVERT: L 35 TRP cc_start: 0.7019 (m100) cc_final: 0.6495 (m100) REVERT: L 75 ILE cc_start: 0.5865 (mm) cc_final: 0.5457 (mt) REVERT: L 103 LYS cc_start: 0.6643 (mmtt) cc_final: 0.6439 (mmmm) REVERT: M 13 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7256 (mp10) REVERT: M 53 ASP cc_start: 0.7912 (t0) cc_final: 0.7613 (t0) REVERT: N 24 LYS cc_start: 0.8288 (tptt) cc_final: 0.7536 (mtmm) REVERT: N 75 ILE cc_start: 0.8137 (mt) cc_final: 0.7794 (tt) outliers start: 45 outliers final: 34 residues processed: 287 average time/residue: 0.3457 time to fit residues: 149.0651 Evaluate side-chains 288 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 252 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 71 optimal weight: 0.9990 chunk 190 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS C 72 HIS E 82 GLN F 651 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19670 Z= 0.268 Angle : 0.677 13.155 26694 Z= 0.326 Chirality : 0.050 0.437 3394 Planarity : 0.004 0.047 3203 Dihedral : 9.225 67.460 5115 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.60 % Allowed : 12.45 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.14 % 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: -1.88 (0.17), residues: 2192 helix: 0.02 (0.28), residues: 352 sheet: -1.23 (0.20), residues: 605 loop : -1.65 (0.16), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 338 HIS 0.005 0.001 HIS C 374 PHE 0.022 0.002 PHE N 49 TYR 0.021 0.002 TYR C 191 ARG 0.004 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 251 time to evaluate : 2.276 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: B 621 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7684 (tm-30) REVERT: C 378 CYS cc_start: 0.6196 (t) cc_final: 0.5859 (t) REVERT: E 191 TYR cc_start: 0.8502 (m-80) cc_final: 0.8265 (m-80) REVERT: E 486 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.7040 (p90) REVERT: F 545 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9046 (tm) REVERT: F 567 ARG cc_start: 0.6227 (ptm160) cc_final: 0.5873 (ptp-110) REVERT: F 620 ASP cc_start: 0.8145 (t0) cc_final: 0.7914 (t0) REVERT: H 67 PHE cc_start: 0.8491 (m-10) cc_final: 0.8241 (m-80) REVERT: H 81 GLU cc_start: 0.7428 (tp30) cc_final: 0.7115 (mm-30) REVERT: L 75 ILE cc_start: 0.5659 (mm) cc_final: 0.5239 (mt) REVERT: M 13 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7252 (mp10) REVERT: M 53 ASP cc_start: 0.7946 (t0) cc_final: 0.7643 (t0) REVERT: N 24 LYS cc_start: 0.8319 (tptt) cc_final: 0.7545 (mtmm) REVERT: N 75 ILE cc_start: 0.8124 (mt) cc_final: 0.7741 (tt) outliers start: 49 outliers final: 41 residues processed: 279 average time/residue: 0.3311 time to fit residues: 138.7381 Evaluate side-chains 286 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 243 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 204 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 120 optimal weight: 0.8980 chunk 154 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 chunk 118 optimal weight: 0.1980 chunk 211 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS E 82 GLN F 651 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82AASN M 105 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19670 Z= 0.231 Angle : 0.651 13.084 26694 Z= 0.312 Chirality : 0.049 0.421 3394 Planarity : 0.004 0.046 3203 Dihedral : 8.751 65.815 5115 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.86 % Allowed : 12.65 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.05 % 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: -1.72 (0.17), residues: 2192 helix: 0.17 (0.28), residues: 352 sheet: -1.06 (0.21), residues: 591 loop : -1.59 (0.16), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP N 35 HIS 0.004 0.001 HIS C 374 PHE 0.021 0.002 PHE N 49 TYR 0.020 0.001 TYR C 191 ARG 0.004 0.000 ARG N 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 263 time to evaluate : 2.133 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: A 195 ASN cc_start: 0.8155 (m-40) cc_final: 0.7733 (m-40) REVERT: A 199 SER cc_start: 0.8371 (m) cc_final: 0.8151 (t) REVERT: B 621 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7710 (tm-30) REVERT: C 378 CYS cc_start: 0.6210 (t) cc_final: 0.5918 (t) REVERT: E 153 GLU cc_start: 0.7609 (pp20) cc_final: 0.7005 (pp20) REVERT: E 191 TYR cc_start: 0.8623 (m-80) cc_final: 0.8291 (m-80) REVERT: E 199 SER cc_start: 0.8588 (OUTLIER) cc_final: 0.8339 (p) REVERT: E 486 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.7037 (p90) REVERT: F 545 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9071 (tm) REVERT: F 567 ARG cc_start: 0.6376 (ptm160) cc_final: 0.5933 (ptp-110) REVERT: F 620 ASP cc_start: 0.8112 (t0) cc_final: 0.7877 (t0) REVERT: H 67 PHE cc_start: 0.8466 (m-10) cc_final: 0.7953 (m-80) REVERT: H 81 GLU cc_start: 0.7447 (tp30) cc_final: 0.7116 (mm-30) REVERT: H 82 MET cc_start: 0.7244 (mmm) cc_final: 0.7043 (mmm) REVERT: L 33 LEU cc_start: 0.7644 (tp) cc_final: 0.7441 (tp) REVERT: L 75 ILE cc_start: 0.5821 (mm) cc_final: 0.5440 (mt) REVERT: M 13 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7245 (mp10) REVERT: M 53 ASP cc_start: 0.7936 (t0) cc_final: 0.7622 (t0) REVERT: N 24 LYS cc_start: 0.8318 (tptt) cc_final: 0.7593 (mtmm) REVERT: N 75 ILE cc_start: 0.8186 (mt) cc_final: 0.7813 (tt) outliers start: 54 outliers final: 42 residues processed: 291 average time/residue: 0.3146 time to fit residues: 138.1196 Evaluate side-chains 294 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 249 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 0.3980 chunk 84 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 104 optimal weight: 0.0170 chunk 19 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN C 72 HIS F 651 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19670 Z= 0.181 Angle : 0.625 12.910 26694 Z= 0.298 Chirality : 0.048 0.393 3394 Planarity : 0.004 0.046 3203 Dihedral : 8.228 63.421 5115 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.19 % Allowed : 13.32 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.09 % 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: -1.52 (0.18), residues: 2192 helix: 0.42 (0.29), residues: 352 sheet: -0.96 (0.21), residues: 608 loop : -1.47 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 35 HIS 0.003 0.001 HIS A 374 PHE 0.020 0.002 PHE N 49 TYR 0.018 0.001 TYR C 191 ARG 0.006 0.000 ARG M 100C *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 278 time to evaluate : 2.173 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: A 195 ASN cc_start: 0.8033 (m-40) cc_final: 0.7625 (m-40) REVERT: B 621 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7714 (tm-30) REVERT: E 153 GLU cc_start: 0.7490 (pp20) cc_final: 0.6959 (pp20) REVERT: E 191 TYR cc_start: 0.8592 (m-80) cc_final: 0.8322 (m-80) REVERT: E 199 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.8130 (p) REVERT: E 486 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.7191 (p90) REVERT: F 545 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9056 (tm) REVERT: F 567 ARG cc_start: 0.6218 (ptm160) cc_final: 0.5883 (ptp-110) REVERT: H 67 PHE cc_start: 0.8422 (m-10) cc_final: 0.7826 (m-80) REVERT: L 39 LYS cc_start: 0.7680 (mtpp) cc_final: 0.7217 (mtpp) REVERT: L 75 ILE cc_start: 0.5944 (mm) cc_final: 0.5588 (mt) REVERT: M 13 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7348 (mp10) REVERT: M 34 MET cc_start: 0.8466 (mmt) cc_final: 0.8236 (mmt) REVERT: M 53 ASP cc_start: 0.7831 (t0) cc_final: 0.7509 (t0) REVERT: N 24 LYS cc_start: 0.8316 (tptt) cc_final: 0.7595 (mtmm) REVERT: N 75 ILE cc_start: 0.8095 (mt) cc_final: 0.7630 (tt) outliers start: 41 outliers final: 32 residues processed: 298 average time/residue: 0.3259 time to fit residues: 146.8138 Evaluate side-chains 289 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 254 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 184 optimal weight: 9.9990 chunk 196 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS E 66 HIS E 82 GLN E 249 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN F 651 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 19670 Z= 0.496 Angle : 0.820 14.328 26694 Z= 0.395 Chirality : 0.054 0.513 3394 Planarity : 0.005 0.056 3203 Dihedral : 9.107 66.694 5115 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.81 % Allowed : 13.57 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.14 % 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: -1.82 (0.17), residues: 2192 helix: -0.10 (0.28), residues: 357 sheet: -1.04 (0.21), residues: 597 loop : -1.64 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 96 HIS 0.011 0.002 HIS H 56 PHE 0.029 0.003 PHE H 96 TYR 0.028 0.003 TYR C 191 ARG 0.008 0.001 ARG M 100C *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 236 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8012 (tppt) REVERT: B 621 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7796 (tm-30) REVERT: C 378 CYS cc_start: 0.6230 (t) cc_final: 0.5961 (t) REVERT: E 153 GLU cc_start: 0.7611 (pp20) cc_final: 0.6881 (pp20) REVERT: E 191 TYR cc_start: 0.8720 (m-80) cc_final: 0.8395 (m-80) REVERT: E 486 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.6864 (p90) REVERT: F 545 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9127 (tm) REVERT: F 567 ARG cc_start: 0.6154 (ptm160) cc_final: 0.5872 (ptp-110) REVERT: H 67 PHE cc_start: 0.8434 (m-10) cc_final: 0.8138 (m-80) REVERT: L 39 LYS cc_start: 0.7729 (mtpp) cc_final: 0.7259 (mtpp) REVERT: M 13 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7270 (mp10) REVERT: M 53 ASP cc_start: 0.8029 (t0) cc_final: 0.7742 (t0) REVERT: N 24 LYS cc_start: 0.8362 (tptt) cc_final: 0.7696 (mtmm) outliers start: 53 outliers final: 45 residues processed: 270 average time/residue: 0.3284 time to fit residues: 133.4567 Evaluate side-chains 279 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 231 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 620 ASP Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 3.9990 chunk 126 optimal weight: 0.0010 chunk 98 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 218 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 173 optimal weight: 0.3980 chunk 18 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS E 82 GLN F 577 GLN F 651 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19670 Z= 0.174 Angle : 0.644 13.147 26694 Z= 0.307 Chirality : 0.048 0.386 3394 Planarity : 0.004 0.053 3203 Dihedral : 8.125 63.412 5115 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.79 % Allowed : 15.10 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.09 % 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: -1.48 (0.17), residues: 2192 helix: 0.43 (0.29), residues: 349 sheet: -0.84 (0.21), residues: 599 loop : -1.49 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 35 HIS 0.004 0.001 HIS A 374 PHE 0.018 0.001 PHE N 49 TYR 0.029 0.001 TYR B 644 ARG 0.006 0.000 ARG M 100C ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 264 time to evaluate : 2.195 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: A 195 ASN cc_start: 0.8050 (m-40) cc_final: 0.7659 (m-40) REVERT: E 153 GLU cc_start: 0.7536 (pp20) cc_final: 0.6971 (pp20) REVERT: E 191 TYR cc_start: 0.8625 (m-80) cc_final: 0.8348 (m-80) REVERT: E 199 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.8133 (p) REVERT: E 486 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.7062 (p90) REVERT: F 545 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9067 (tm) REVERT: F 567 ARG cc_start: 0.6230 (ptm160) cc_final: 0.5898 (ptp-110) REVERT: H 64 GLN cc_start: 0.8269 (tp-100) cc_final: 0.8051 (tp-100) REVERT: L 39 LYS cc_start: 0.7745 (mtpp) cc_final: 0.7263 (mtpp) REVERT: L 75 ILE cc_start: 0.6049 (mm) cc_final: 0.5679 (mt) REVERT: M 13 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7262 (mp10) REVERT: M 53 ASP cc_start: 0.7819 (t0) cc_final: 0.7525 (t0) REVERT: M 95 MET cc_start: 0.8226 (ttp) cc_final: 0.7988 (ttp) REVERT: N 24 LYS cc_start: 0.8329 (tptt) cc_final: 0.7650 (mtmm) REVERT: N 75 ILE cc_start: 0.7892 (mt) cc_final: 0.7665 (tt) outliers start: 33 outliers final: 27 residues processed: 281 average time/residue: 0.3273 time to fit residues: 137.8838 Evaluate side-chains 283 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 253 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 0.1980 chunk 53 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 22 optimal weight: 0.0870 chunk 32 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS E 249 HIS F 651 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.139330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.108248 restraints weight = 90219.421| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 5.06 r_work: 0.3177 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19670 Z= 0.213 Angle : 0.651 13.067 26694 Z= 0.310 Chirality : 0.048 0.409 3394 Planarity : 0.004 0.049 3203 Dihedral : 8.018 63.038 5115 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.94 % Allowed : 15.05 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.39 (0.17), residues: 2192 helix: 0.55 (0.29), residues: 350 sheet: -0.76 (0.22), residues: 586 loop : -1.46 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 35 HIS 0.004 0.001 HIS A 374 PHE 0.020 0.002 PHE N 49 TYR 0.020 0.001 TYR B 638 ARG 0.006 0.000 ARG M 100C Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4321.24 seconds wall clock time: 79 minutes 37.05 seconds (4777.05 seconds total)