Starting phenix.real_space_refine on Sat Mar 16 20:57:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l87_23224/03_2024/7l87_23224_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l87_23224/03_2024/7l87_23224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l87_23224/03_2024/7l87_23224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l87_23224/03_2024/7l87_23224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l87_23224/03_2024/7l87_23224_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l87_23224/03_2024/7l87_23224_updated.pdb" } resolution = 3.6 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 9809 2.51 5 N 2631 2.21 5 O 3227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 87": "OE1" <-> "OE2" Residue "C ASP 457": "OD1" <-> "OD2" Residue "E ARG 617": "NH1" <-> "NH2" Residue "E GLU 634": "OE1" <-> "OE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A ARG 503": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15766 Number of models: 1 Model: "" Number of chains: 53 Chain: "H" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 605 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'TRANS': 120} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 121 Planarities with less than four sites: {'UNK:plan-1': 121} Unresolved non-hydrogen planarities: 121 Chain: "L" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 515 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'TRANS': 102} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 103 Planarities with less than four sites: {'UNK:plan-1': 103} Unresolved non-hydrogen planarities: 103 Chain: "C" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "A" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "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: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" 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: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.58, per 1000 atoms: 0.54 Number of scatterers: 15766 At special positions: 0 Unit cell: (130.81, 132.87, 118.45, 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 99 16.00 O 3227 8.00 N 2631 7.00 C 9809 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.05 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.05 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.04 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.07 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Z 3 " - " MAN Z 4 " " BMA m 3 " - " MAN m 4 " ALPHA1-6 " BMA Z 3 " - " MAN Z 5 " " BMA m 3 " - " MAN m 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " NAG-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 355 " " NAG B 701 " - " ASN B 611 " " NAG C 601 " - " ASN C 160 " " NAG C 602 " - " ASN C 339 " " NAG C 603 " - " ASN C 355 " " NAG D 601 " - " ASN D 160 " " NAG D 602 " - " ASN D 339 " " NAG D 603 " - " ASN D 137 " " NAG E 701 " - " ASN E 611 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN C 133 " " NAG I 1 " - " ASN C 156 " " NAG J 1 " - " ASN C 197 " " NAG K 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 262 " " NAG N 1 " - " ASN C 276 " " NAG O 1 " - " ASN C 295 " " NAG P 1 " - " ASN C 301 " " NAG Q 1 " - " ASN C 332 " " NAG R 1 " - " ASN C 386 " " NAG S 1 " - " ASN C 392 " " NAG T 1 " - " ASN C 448 " " NAG U 1 " - " ASN C 88 " " NAG V 1 " - " ASN A 133 " " NAG W 1 " - " ASN A 156 " " NAG X 1 " - " ASN A 197 " " NAG Y 1 " - " ASN A 234 " " NAG Z 1 " - " ASN A 262 " " NAG a 1 " - " ASN A 276 " " NAG b 1 " - " ASN A 295 " " NAG c 1 " - " ASN A 301 " " NAG d 1 " - " ASN A 332 " " NAG e 1 " - " ASN A 386 " " NAG f 1 " - " ASN A 392 " " NAG g 1 " - " ASN A 448 " " NAG h 1 " - " ASN A 88 " " NAG i 1 " - " ASN D 133 " " NAG j 1 " - " ASN D 156 " " NAG k 1 " - " ASN D 197 " " NAG l 1 " - " ASN D 234 " " NAG m 1 " - " ASN D 262 " " NAG n 1 " - " ASN D 276 " " NAG o 1 " - " ASN D 295 " " NAG p 1 " - " ASN D 301 " " NAG q 1 " - " ASN D 332 " " NAG r 1 " - " ASN D 386 " " NAG s 1 " - " ASN D 392 " " NAG t 1 " - " ASN D 448 " " NAG u 1 " - " ASN D 88 " Time building additional restraints: 7.65 Conformation dependent library (CDL) restraints added in 2.3 seconds 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3592 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 32 sheets defined 26.4% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.704A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (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 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 194 through 197 removed outlier: 4.423A pdb=" N ASN C 197 " --> pdb=" O ILE C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.529A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (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 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 475 through 485 removed outlier: 4.787A pdb=" N TYR C 484 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 541 removed outlier: 4.874A pdb=" N MET E 535 " --> pdb=" O GLY E 531 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR E 536 " --> pdb=" O ALA E 532 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU E 537 " --> pdb=" O ALA E 533 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N THR E 538 " --> pdb=" O SER E 534 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL E 539 " --> pdb=" O MET E 535 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 595 removed outlier: 4.039A pdb=" N LEU E 576 " --> pdb=" O ILE E 573 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS E 585 " --> pdb=" O ALA E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 625 removed outlier: 3.990A pdb=" N ASP E 624 " --> pdb=" O SER E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 628 through 662 removed outlier: 5.187A pdb=" N ASN E 637 " --> pdb=" O LYS E 633 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR E 638 " --> pdb=" O GLU E 634 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR E 639 " --> pdb=" O ILE E 635 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLN E 640 " --> pdb=" O SER E 636 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE E 641 " --> pdb=" O ASN E 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 99 through 115 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 140 through 150 No H-bonds generated for 'chain 'A' and resid 140 through 150' 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 194 through 197 removed outlier: 4.242A pdb=" N ASN A 197 " --> pdb=" O ILE A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 335 through 353 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 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'B' and resid 522 through 525 removed outlier: 4.310A pdb=" N ALA B 525 " --> pdb=" O PHE B 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 522 through 525' Processing helix chain 'B' and resid 530 through 535 removed outlier: 4.488A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 removed outlier: 4.455A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 595 removed outlier: 3.567A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 639 through 662 removed outlier: 3.531A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'D' and resid 99 through 116 removed outlier: 3.669A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 125 No H-bonds generated for 'chain 'D' and resid 123 through 125' Processing helix chain 'D' and resid 194 through 197 removed outlier: 4.282A pdb=" N ASN D 197 " --> pdb=" O ILE D 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 194 through 197' Processing helix chain 'D' and resid 335 through 353 Processing helix chain 'D' and resid 369 through 372 No H-bonds generated for 'chain 'D' and resid 369 through 372' Processing helix chain 'D' and resid 426 through 428 No H-bonds generated for 'chain 'D' and resid 426 through 428' Processing helix chain 'D' and resid 475 through 481 removed outlier: 3.517A pdb=" N TRP D 479 " --> pdb=" O ARG D 476 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG D 480 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 543 removed outlier: 3.959A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU F 537 " --> pdb=" O ALA F 533 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL F 539 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 595 removed outlier: 3.859A pdb=" N GLN F 575 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN F 577 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL F 580 " --> pdb=" O GLN F 577 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS F 585 " --> pdb=" O ALA F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 623 Processing helix chain 'F' and resid 628 through 663 removed outlier: 5.016A pdb=" N ASN F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR F 639 " --> pdb=" O ILE F 635 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLN F 640 " --> pdb=" O SER F 636 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'H' and resid 5 through 8 removed outlier: 3.591A pdb=" N UNK H 20 " --> pdb=" O UNK H 81 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N UNK H 78 " --> pdb=" O UNK H 74 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 97 through 100 removed outlier: 3.500A pdb=" N UNK H 35 " --> pdb=" O UNK H 100 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N UNK H 52 " --> pdb=" O UNK H 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L' and resid 20 through 24 removed outlier: 3.631A pdb=" N UNK L 73 " --> pdb=" O UNK L 66 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 86 through 90 removed outlier: 3.640A pdb=" N UNK L 36 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N UNK L 38 " --> pdb=" O UNK L 47 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N UNK L 47 " --> pdb=" O UNK L 38 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= F, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.866A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= H, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= I, first strand: chain 'C' and resid 200 through 203 Processing sheet with id= J, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.654A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 443 through 449 removed outlier: 7.262A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 465 through 469 removed outlier: 6.284A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.019A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 53 through 56 removed outlier: 5.495A pdb=" N HIS C 216 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 302 through 308 removed outlier: 5.943A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= Q, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.709A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= S, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= T, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= U, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.706A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.423A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N ALA A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.812A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 301 through 308 removed outlier: 4.492A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 35 through 40 Processing sheet with id= Z, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.727A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 130 through 133 Processing sheet with id= AB, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= AC, first strand: chain 'D' and resid 201 through 203 removed outlier: 6.747A pdb=" N ALA D 433 " --> pdb=" O THR D 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'D' and resid 272 through 274 Processing sheet with id= AE, first strand: chain 'D' and resid 374 through 378 removed outlier: 3.903A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 301 through 308 removed outlier: 4.101A pdb=" N ASN D 301 " --> pdb=" O ILE D 323A" (cutoff:3.500A) removed outlier: 5.842A pdb=" N LYS D 305 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR D 320 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE D 307 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N TYR D 318 " --> pdb=" O ILE D 307 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1263 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: 4.86 Time building geometry restraints manager: 8.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2642 1.31 - 1.45: 4825 1.45 - 1.59: 8369 1.59 - 1.73: 70 1.73 - 1.87: 128 Bond restraints: 16034 Sorted by residual: bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.401 -0.075 1.10e-02 8.26e+03 4.68e+01 bond pdb=" NE ARG D 503 " pdb=" CZ ARG D 503 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.55e+01 bond pdb=" CB LEU A 129 " pdb=" CG LEU A 129 " ideal model delta sigma weight residual 1.530 1.406 0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" C GLN C 170 " pdb=" O GLN C 170 " ideal model delta sigma weight residual 1.235 1.166 0.069 1.13e-02 7.83e+03 3.75e+01 bond pdb=" NE1 TRP E 631 " pdb=" CE2 TRP E 631 " ideal model delta sigma weight residual 1.370 1.307 0.063 1.10e-02 8.26e+03 3.29e+01 ... (remaining 16029 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.60: 400 105.60 - 112.92: 8809 112.92 - 120.24: 6571 120.24 - 127.56: 5836 127.56 - 134.88: 197 Bond angle restraints: 21813 Sorted by residual: angle pdb=" C ASN D 137 " pdb=" N ILE D 138 " pdb=" CA ILE D 138 " ideal model delta sigma weight residual 120.98 134.88 -13.90 1.36e+00 5.41e-01 1.04e+02 angle pdb=" N ILE A 184 " pdb=" CA ILE A 184 " pdb=" C ILE A 184 " ideal model delta sigma weight residual 110.62 119.23 -8.61 1.02e+00 9.61e-01 7.13e+01 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 127.21 -7.65 1.02e+00 9.61e-01 5.62e+01 angle pdb=" C CYS D 239 " pdb=" N PRO D 240 " pdb=" CA PRO D 240 " ideal model delta sigma weight residual 119.56 127.15 -7.59 1.02e+00 9.61e-01 5.53e+01 angle pdb=" N LEU B 544 " pdb=" CA LEU B 544 " pdb=" C LEU B 544 " ideal model delta sigma weight residual 110.48 99.70 10.78 1.48e+00 4.57e-01 5.31e+01 ... (remaining 21808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 10589 21.62 - 43.24: 246 43.24 - 64.86: 57 64.86 - 86.48: 51 86.48 - 108.10: 25 Dihedral angle restraints: 10968 sinusoidal: 5453 harmonic: 5515 Sorted by residual: dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.79 -57.79 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 148.90 -55.90 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 145.47 -52.47 1 1.00e+01 1.00e-02 3.75e+01 ... (remaining 10965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.171: 2236 0.171 - 0.341: 447 0.341 - 0.511: 124 0.511 - 0.682: 4 0.682 - 0.852: 2 Chirality restraints: 2813 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.45e+02 chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.63e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.49e+02 ... (remaining 2810 not shown) Planarity restraints: 2711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.351 2.00e-02 2.50e+03 3.03e-01 1.14e+03 pdb=" C7 NAG M 1 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " -0.086 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " 0.347 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG O 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " 0.134 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " 0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 604 " -0.344 2.00e-02 2.50e+03 2.97e-01 1.11e+03 pdb=" C7 NAG A 604 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG A 604 " -0.068 2.00e-02 2.50e+03 pdb=" N2 NAG A 604 " 0.525 2.00e-02 2.50e+03 pdb=" O7 NAG A 604 " -0.193 2.00e-02 2.50e+03 ... (remaining 2708 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 114 2.60 - 3.18: 13558 3.18 - 3.75: 22214 3.75 - 4.33: 33376 4.33 - 4.90: 51912 Nonbonded interactions: 121174 Sorted by model distance: nonbonded pdb=" NZ LYS A 502 " pdb=" O ASP F 664 " model vdw 2.027 2.520 nonbonded pdb=" O4 MAN M 4 " pdb=" O6 MAN M 4 " model vdw 2.308 2.440 nonbonded pdb=" O PHE E 522 " pdb=" NE2 GLN E 540 " model vdw 2.312 2.520 nonbonded pdb=" O SER D 463 " pdb=" OG SER D 463 " model vdw 2.354 2.440 nonbonded pdb=" O HIS B 570 " pdb=" N LYS B 574 " model vdw 2.402 2.520 ... (remaining 121169 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 33 through 503 or resid 601 through 603)) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' } ncs_group { reference = (chain 'H' and resid 19 through 121) selection = chain 'L' } ncs_group { reference = chain 'Q' selection = chain 'd' selection = chain 'q' } ncs_group { reference = chain 'Z' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.630 Check model and map are aligned: 0.190 Set scattering table: 0.160 Process input model: 44.530 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.310 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.023 0.132 16034 Z= 1.407 Angle : 1.760 20.202 21813 Z= 1.097 Chirality : 0.152 0.852 2813 Planarity : 0.016 0.303 2659 Dihedral : 12.583 108.101 7277 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.19), residues: 1635 helix: 0.10 (0.24), residues: 399 sheet: 1.15 (0.28), residues: 312 loop : 0.60 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.008 TRP C 96 HIS 0.018 0.003 HIS A 374 PHE 0.052 0.006 PHE A 159 TYR 0.036 0.007 TYR A 384 ARG 0.010 0.001 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 180 ASP cc_start: 0.8007 (m-30) cc_final: 0.7650 (m-30) REVERT: C 198 THR cc_start: 0.8988 (p) cc_final: 0.8633 (p) REVERT: B 632 ASP cc_start: 0.8295 (t70) cc_final: 0.8035 (t0) REVERT: B 652 GLN cc_start: 0.7855 (mt0) cc_final: 0.7514 (mt0) REVERT: B 660 LEU cc_start: 0.8970 (mt) cc_final: 0.8747 (tt) REVERT: D 122 LEU cc_start: 0.8864 (mt) cc_final: 0.8605 (mp) REVERT: F 590 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8683 (mm110) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.3087 time to fit residues: 179.0237 Evaluate side-chains 183 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN C 363 GLN C 425 ASN E 590 GLN A 33 ASN A 428 GLN D 352 HIS D 428 GLN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 570 HIS F 651 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16034 Z= 0.219 Angle : 0.717 14.650 21813 Z= 0.351 Chirality : 0.047 0.228 2813 Planarity : 0.004 0.052 2659 Dihedral : 9.839 82.396 4112 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.90 % Favored : 98.04 % Rotamer: Outliers : 2.61 % Allowed : 8.03 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1635 helix: 0.94 (0.27), residues: 399 sheet: 1.14 (0.24), residues: 405 loop : 0.20 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 571 HIS 0.009 0.001 HIS F 570 PHE 0.034 0.002 PHE A 159 TYR 0.009 0.001 TYR A 484 ARG 0.010 0.001 ARG E 588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 242 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 634 GLU cc_start: 0.8169 (tt0) cc_final: 0.7918 (mt-10) REVERT: A 246 GLN cc_start: 0.7077 (tp-100) cc_final: 0.6867 (tp-100) REVERT: A 384 TYR cc_start: 0.8844 (m-80) cc_final: 0.8616 (m-80) REVERT: B 632 ASP cc_start: 0.8347 (t70) cc_final: 0.8137 (t0) REVERT: D 150 MET cc_start: 0.7599 (mmp) cc_final: 0.7234 (mmt) REVERT: D 167 ASP cc_start: 0.7530 (p0) cc_final: 0.7288 (p0) REVERT: D 434 MET cc_start: 0.8430 (ttp) cc_final: 0.8119 (ttt) REVERT: F 542 ARG cc_start: 0.8796 (ptp90) cc_final: 0.8576 (ptt180) outliers start: 39 outliers final: 26 residues processed: 269 average time/residue: 0.2683 time to fit residues: 106.9354 Evaluate side-chains 205 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 179 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 GLN A 33 ASN A 216 HIS D 80 ASN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 570 HIS F 651 ASN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16034 Z= 0.320 Angle : 0.696 9.622 21813 Z= 0.348 Chirality : 0.047 0.322 2813 Planarity : 0.004 0.047 2659 Dihedral : 8.609 79.810 4112 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.08 % Allowed : 9.10 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.21), residues: 1635 helix: 0.94 (0.27), residues: 384 sheet: 1.13 (0.24), residues: 405 loop : -0.09 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 571 HIS 0.012 0.002 HIS F 570 PHE 0.042 0.002 PHE A 159 TYR 0.014 0.001 TYR D 173 ARG 0.006 0.001 ARG E 588 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 187 time to evaluate : 1.699 Fit side-chains revert: symmetry clash REVERT: C 150 MET cc_start: 0.8733 (mtp) cc_final: 0.8513 (mtt) REVERT: B 520 LEU cc_start: 0.8351 (mm) cc_final: 0.7829 (mt) REVERT: D 167 ASP cc_start: 0.7710 (p0) cc_final: 0.7409 (p0) REVERT: D 332 ASN cc_start: 0.8031 (m-40) cc_final: 0.7543 (m-40) REVERT: D 434 MET cc_start: 0.8395 (ttp) cc_final: 0.7927 (ttt) REVERT: F 542 ARG cc_start: 0.8924 (ptp90) cc_final: 0.8706 (ptt180) outliers start: 61 outliers final: 44 residues processed: 233 average time/residue: 0.2567 time to fit residues: 90.5452 Evaluate side-chains 206 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 162 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 170 optimal weight: 7.9990 chunk 180 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 HIS F 651 ASN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16034 Z= 0.220 Angle : 0.608 8.622 21813 Z= 0.301 Chirality : 0.045 0.243 2813 Planarity : 0.004 0.048 2659 Dihedral : 7.853 75.666 4112 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.08 % Allowed : 11.71 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1635 helix: 1.18 (0.29), residues: 366 sheet: 0.96 (0.24), residues: 417 loop : -0.13 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 338 HIS 0.006 0.001 HIS F 570 PHE 0.038 0.002 PHE A 159 TYR 0.010 0.001 TYR D 191 ARG 0.003 0.000 ARG D 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 174 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 370 GLU cc_start: 0.8137 (tt0) cc_final: 0.7903 (tt0) REVERT: C 426 MET cc_start: 0.8062 (mtp) cc_final: 0.7772 (mtp) REVERT: A 268 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7763 (mm-30) REVERT: B 520 LEU cc_start: 0.8301 (mm) cc_final: 0.7799 (mt) REVERT: D 137 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.7381 (m-40) REVERT: D 332 ASN cc_start: 0.8048 (m-40) cc_final: 0.7639 (m-40) REVERT: D 434 MET cc_start: 0.8363 (ttp) cc_final: 0.7908 (ttt) REVERT: F 535 MET cc_start: 0.8481 (mpp) cc_final: 0.8154 (mpp) outliers start: 46 outliers final: 32 residues processed: 209 average time/residue: 0.2580 time to fit residues: 81.6326 Evaluate side-chains 185 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 152 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 2 optimal weight: 20.0000 chunk 134 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 162 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN B 543 ASN D 80 ASN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 570 HIS ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16034 Z= 0.329 Angle : 0.669 7.882 21813 Z= 0.329 Chirality : 0.046 0.249 2813 Planarity : 0.004 0.047 2659 Dihedral : 7.662 71.068 4112 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.22 % Allowed : 11.78 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1635 helix: 1.08 (0.28), residues: 363 sheet: 0.53 (0.24), residues: 420 loop : -0.35 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 631 HIS 0.007 0.001 HIS D 330 PHE 0.044 0.002 PHE A 159 TYR 0.017 0.002 TYR C 486 ARG 0.004 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 153 time to evaluate : 1.623 Fit side-chains REVERT: C 426 MET cc_start: 0.8126 (mtp) cc_final: 0.7906 (mtp) REVERT: A 268 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7940 (mm-30) REVERT: D 137 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7302 (m-40) REVERT: D 332 ASN cc_start: 0.8179 (m-40) cc_final: 0.7843 (m-40) REVERT: D 434 MET cc_start: 0.8390 (ttp) cc_final: 0.8052 (ttt) outliers start: 63 outliers final: 46 residues processed: 201 average time/residue: 0.2679 time to fit residues: 81.7818 Evaluate side-chains 190 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 143 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 180 optimal weight: 0.4980 chunk 150 optimal weight: 0.0050 chunk 83 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN C 99 ASN C 289 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN D 80 ASN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 570 HIS ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16034 Z= 0.186 Angle : 0.578 9.108 21813 Z= 0.287 Chirality : 0.044 0.251 2813 Planarity : 0.003 0.045 2659 Dihedral : 7.164 65.702 4112 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.95 % Allowed : 14.12 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1635 helix: 1.26 (0.29), residues: 363 sheet: 0.44 (0.24), residues: 414 loop : -0.40 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 338 HIS 0.006 0.001 HIS F 570 PHE 0.037 0.002 PHE A 159 TYR 0.015 0.001 TYR A 173 ARG 0.002 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 162 time to evaluate : 1.581 Fit side-chains REVERT: C 82 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7847 (pm20) REVERT: C 426 MET cc_start: 0.8096 (mtp) cc_final: 0.7833 (mtp) REVERT: E 540 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8477 (mp10) REVERT: A 92 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7652 (mm-30) REVERT: A 268 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7986 (mm-30) REVERT: B 601 LYS cc_start: 0.8340 (mtpp) cc_final: 0.8107 (mtpp) REVERT: D 332 ASN cc_start: 0.8139 (m-40) cc_final: 0.7928 (m-40) REVERT: D 434 MET cc_start: 0.8369 (ttp) cc_final: 0.8059 (ttt) outliers start: 44 outliers final: 31 residues processed: 196 average time/residue: 0.2648 time to fit residues: 77.4669 Evaluate side-chains 182 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 148 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 152 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN F 543 ASN F 570 HIS ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16034 Z= 0.197 Angle : 0.573 7.189 21813 Z= 0.284 Chirality : 0.044 0.279 2813 Planarity : 0.003 0.045 2659 Dihedral : 6.945 60.613 4112 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.28 % Allowed : 14.46 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1635 helix: 1.32 (0.29), residues: 363 sheet: 0.42 (0.24), residues: 414 loop : -0.42 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 571 HIS 0.004 0.001 HIS F 570 PHE 0.038 0.002 PHE A 159 TYR 0.013 0.001 TYR A 173 ARG 0.002 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 156 time to evaluate : 1.677 Fit side-chains REVERT: E 540 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8397 (mp10) REVERT: A 92 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7665 (mm-30) REVERT: A 268 GLU cc_start: 0.8213 (mm-30) cc_final: 0.8011 (mm-30) REVERT: B 601 LYS cc_start: 0.8418 (mtpp) cc_final: 0.7734 (mttm) REVERT: B 602 LEU cc_start: 0.8624 (mt) cc_final: 0.8380 (mt) REVERT: B 625 ASN cc_start: 0.8236 (t0) cc_final: 0.8005 (t0) REVERT: D 434 MET cc_start: 0.8382 (ttp) cc_final: 0.8074 (ttt) outliers start: 49 outliers final: 42 residues processed: 193 average time/residue: 0.2738 time to fit residues: 79.2107 Evaluate side-chains 193 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 149 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 114 optimal weight: 0.0670 chunk 122 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN C 99 ASN C 289 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 570 HIS ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16034 Z= 0.284 Angle : 0.624 8.290 21813 Z= 0.308 Chirality : 0.045 0.234 2813 Planarity : 0.004 0.045 2659 Dihedral : 6.966 59.413 4112 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.75 % Allowed : 14.39 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.21), residues: 1635 helix: 1.27 (0.29), residues: 363 sheet: 0.37 (0.24), residues: 408 loop : -0.56 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 571 HIS 0.023 0.001 HIS F 570 PHE 0.041 0.002 PHE A 159 TYR 0.010 0.001 TYR C 486 ARG 0.003 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 154 time to evaluate : 1.672 Fit side-chains REVERT: C 136 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7436 (m-40) REVERT: A 207 LYS cc_start: 0.8016 (pttt) cc_final: 0.7815 (tmmt) REVERT: A 368 ASP cc_start: 0.6842 (t70) cc_final: 0.5002 (t0) REVERT: B 601 LYS cc_start: 0.8340 (mtpp) cc_final: 0.7797 (mttm) REVERT: B 602 LEU cc_start: 0.8577 (mt) cc_final: 0.8359 (mt) REVERT: B 625 ASN cc_start: 0.8267 (t0) cc_final: 0.8030 (t0) REVERT: D 434 MET cc_start: 0.8476 (ttp) cc_final: 0.8163 (ttt) outliers start: 56 outliers final: 46 residues processed: 196 average time/residue: 0.2655 time to fit residues: 78.0687 Evaluate side-chains 195 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 148 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 7.9990 chunk 172 optimal weight: 0.5980 chunk 157 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 289 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 570 HIS ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16034 Z= 0.188 Angle : 0.576 8.191 21813 Z= 0.287 Chirality : 0.043 0.210 2813 Planarity : 0.003 0.046 2659 Dihedral : 6.623 59.868 4112 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.08 % Allowed : 15.33 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1635 helix: 1.33 (0.29), residues: 363 sheet: 0.37 (0.24), residues: 414 loop : -0.53 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 338 HIS 0.003 0.001 HIS C 216 PHE 0.037 0.002 PHE A 159 TYR 0.010 0.001 TYR A 191 ARG 0.003 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 158 time to evaluate : 1.868 Fit side-chains revert: symmetry clash REVERT: B 601 LYS cc_start: 0.8306 (mtpp) cc_final: 0.7789 (mttm) REVERT: B 625 ASN cc_start: 0.8209 (t0) cc_final: 0.7987 (t0) REVERT: D 434 MET cc_start: 0.8454 (ttp) cc_final: 0.8154 (ttt) REVERT: F 652 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8157 (tm-30) outliers start: 46 outliers final: 41 residues processed: 193 average time/residue: 0.2723 time to fit residues: 78.7621 Evaluate side-chains 191 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 150 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 171 optimal weight: 0.0030 chunk 148 optimal weight: 0.8980 chunk 15 optimal weight: 20.0000 chunk 114 optimal weight: 0.0980 chunk 90 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 289 ASN E 540 GLN ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN D 80 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 570 HIS ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16034 Z= 0.218 Angle : 0.586 8.574 21813 Z= 0.291 Chirality : 0.044 0.197 2813 Planarity : 0.003 0.046 2659 Dihedral : 6.442 59.696 4112 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.15 % Allowed : 15.60 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1635 helix: 1.26 (0.29), residues: 363 sheet: 0.34 (0.25), residues: 396 loop : -0.48 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 571 HIS 0.009 0.001 HIS F 570 PHE 0.038 0.002 PHE A 159 TYR 0.009 0.001 TYR A 191 ARG 0.002 0.000 ARG D 298 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 155 time to evaluate : 1.775 Fit side-chains REVERT: A 92 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7310 (tm-30) REVERT: B 584 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7921 (mp0) REVERT: B 601 LYS cc_start: 0.8267 (mtpp) cc_final: 0.7437 (mttm) REVERT: D 434 MET cc_start: 0.8459 (ttp) cc_final: 0.8162 (ttt) REVERT: F 652 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8314 (tm-30) outliers start: 47 outliers final: 41 residues processed: 190 average time/residue: 0.2684 time to fit residues: 76.5850 Evaluate side-chains 195 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 153 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 570 HIS ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.125131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107692 restraints weight = 27978.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110577 restraints weight = 16249.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112515 restraints weight = 11154.693| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.272 16034 Z= 0.298 Angle : 0.764 65.895 21813 Z= 0.414 Chirality : 0.045 0.748 2813 Planarity : 0.006 0.224 2659 Dihedral : 6.451 59.682 4112 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.28 % Allowed : 15.66 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1635 helix: 1.26 (0.29), residues: 363 sheet: 0.34 (0.25), residues: 396 loop : -0.48 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 96 HIS 0.004 0.001 HIS F 570 PHE 0.038 0.002 PHE A 159 TYR 0.009 0.001 TYR A 191 ARG 0.002 0.000 ARG D 298 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2861.72 seconds wall clock time: 52 minutes 44.05 seconds (3164.05 seconds total)