Starting phenix.real_space_refine on Sat Jan 20 15:03:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8d_23230/01_2024/7l8d_23230_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8d_23230/01_2024/7l8d_23230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8d_23230/01_2024/7l8d_23230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8d_23230/01_2024/7l8d_23230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8d_23230/01_2024/7l8d_23230_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8d_23230/01_2024/7l8d_23230_updated.pdb" } resolution = 4.6 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= 0.002 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 9694 2.51 5 N 2596 2.21 5 O 3175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "E ASP 624": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 15564 Number of models: 1 Model: "" Number of chains: 49 Chain: "H" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 535 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'TRANS': 106} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'UNK:plan-1': 107} Unresolved non-hydrogen planarities: 107 Chain: "L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 510 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'TRANS': 101} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'UNK:plan-1': 102} Unresolved non-hydrogen planarities: 102 Chain: "A" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3408 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 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: "C" Number of atoms: 3422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3422 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 4 Chain: "E" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "D" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3418 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "F" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 954 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} 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: 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: 9 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: 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: 9 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: 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: 9 Unresolved non-hydrogen chiralities: 5 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "D" 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: "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: 9.18, per 1000 atoms: 0.59 Number of scatterers: 15564 At special positions: 0 Unit cell: (130.81, 123.6, 146.26, 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 3175 8.00 N 2596 7.00 C 9694 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 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=2.11 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.15 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.05 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.02 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 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 K 3 " - " MAN K 4 " " BMA Y 3 " - " MAN Y 4 " " BMA h 3 " - " MAN h 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA Y 3 " - " MAN Y 5 " " BMA h 3 " - " MAN h 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 K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " 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 Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " 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 h 2 " - " BMA h 3 " " 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 n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " NAG-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 197 " " NAG A 603 " - " ASN A 339 " " NAG A 604 " - " ASN A 137 " " NAG A 605 " - " ASN A 355 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 160 " " NAG C 602 " - " ASN C 301 " " NAG C 603 " - " ASN C 339 " " NAG C 604 " - " ASN C 448 " " NAG C 605 " - " ASN C 88 " " NAG C 606 " - " ASN C 137 " " NAG D 601 " - " ASN D 160 " " NAG D 602 " - " ASN D 339 " " NAG D 603 " - " ASN D 137 " " NAG D 604 " - " ASN D 355 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 618 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN A 133 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 276 " " NAG N 1 " - " ASN A 295 " " NAG O 1 " - " ASN A 301 " " NAG P 1 " - " ASN A 332 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 392 " " NAG S 1 " - " ASN A 448 " " NAG T 1 " - " ASN A 88 " " NAG U 1 " - " ASN C 133 " " NAG V 1 " - " ASN C 156 " " NAG W 1 " - " ASN C 197 " " NAG X 1 " - " ASN C 234 " " NAG Y 1 " - " ASN C 262 " " NAG Z 1 " - " ASN C 276 " " NAG a 1 " - " ASN C 295 " " NAG b 1 " - " ASN C 332 " " NAG c 1 " - " ASN C 386 " " NAG d 1 " - " ASN C 392 " " NAG e 1 " - " ASN D 133 " " NAG f 1 " - " ASN D 156 " " NAG g 1 " - " ASN D 197 " " NAG h 1 " - " ASN D 262 " " NAG i 1 " - " ASN D 276 " " NAG j 1 " - " ASN D 295 " " NAG k 1 " - " ASN D 301 " " NAG l 1 " - " ASN D 332 " " NAG m 1 " - " ASN D 386 " " NAG n 1 " - " ASN D 392 " " NAG o 1 " - " ASN D 448 " " NAG p 1 " - " ASN D 88 " " NAG q 1 " - " ASN D 234 " Time building additional restraints: 7.22 Conformation dependent library (CDL) restraints added in 2.5 seconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3534 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 31 sheets defined 26.3% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'H' and resid 59 through 61 No H-bonds generated for 'chain 'H' and resid 59 through 61' Processing helix chain 'L' and resid 27 through 31 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 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 100 through 117 Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.706A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 475 through 485 removed outlier: 3.875A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 525 removed outlier: 4.418A 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 532 through 542 removed outlier: 3.830A pdb=" N LEU B 537 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N THR B 538 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG B 542 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 628 through 663 removed outlier: 3.840A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 639 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLN B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) 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 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 194 through 197 removed outlier: 4.249A 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 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 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: 4.530A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 535 removed outlier: 4.607A pdb=" N MET E 535 " --> pdb=" O GLY E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 543 removed outlier: 3.518A pdb=" N ARG E 542 " --> pdb=" O THR E 538 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 596 removed outlier: 3.574A pdb=" N TRP E 596 " --> pdb=" O LEU E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 622 through 625 No H-bonds generated for 'chain 'E' and resid 622 through 625' Processing helix chain 'E' and resid 628 through 633 Processing helix chain 'E' and resid 639 through 663 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 117 removed outlier: 3.557A pdb=" N ILE D 108 " --> pdb=" O HIS D 105 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS D 117 " --> pdb=" O GLN D 114 " (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 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 335 through 351 removed outlier: 4.059A pdb=" N LYS D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) 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 387 through 389 No H-bonds generated for 'chain 'D' and resid 387 through 389' 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 482 Processing helix chain 'F' and resid 530 through 535 removed outlier: 4.106A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.752A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 595 Processing helix chain 'F' and resid 619 through 622 No H-bonds generated for 'chain 'F' and resid 619 through 622' Processing helix chain 'F' and resid 628 through 634 Processing helix chain 'F' and resid 639 through 660 Processing sheet with id= A, first strand: chain 'H' and resid 18 through 20 removed outlier: 4.425A pdb=" N UNK H 18 " --> pdb=" O UNK H 78 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 90 through 94 Processing sheet with id= C, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= D, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= E, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.652A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= G, first strand: chain 'A' and resid 130 through 133 removed outlier: 4.920A pdb=" N LYS A 168 " --> pdb=" O THR A 163 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= I, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.846A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 271 through 273 Processing sheet with id= K, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.685A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.516A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= N, first strand: chain 'C' and resid 45 through 47 Processing sheet with id= O, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= P, first strand: chain 'C' and resid 91 through 93 Processing sheet with id= Q, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= R, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= S, first strand: chain 'C' and resid 200 through 203 removed outlier: 3.536A pdb=" N ALA C 433 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.584A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 443 through 449 removed outlier: 3.661A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 305 through 312 removed outlier: 6.807A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 35 through 40 Processing sheet with id= X, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= Y, first strand: chain 'D' and resid 53 through 56 Processing sheet with id= Z, first strand: chain 'D' and resid 130 through 133 Processing sheet with id= AA, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= AB, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.289A pdb=" N ILE D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE D 468 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ALA D 362 " --> pdb=" O PRO D 470 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 413 through 417 removed outlier: 4.357A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 374 through 378 removed outlier: 3.909A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 304 through 312 removed outlier: 6.472A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.50 Time building geometry restraints manager: 7.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4565 1.34 - 1.49: 4901 1.49 - 1.64: 6234 1.64 - 1.79: 59 1.79 - 1.95: 73 Bond restraints: 15832 Sorted by residual: bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.03e+01 bond pdb=" CB THR A 37 " pdb=" OG1 THR A 37 " ideal model delta sigma weight residual 1.433 1.339 0.094 1.60e-02 3.91e+03 3.48e+01 bond pdb=" CB LEU C 34 " pdb=" CG LEU C 34 " ideal model delta sigma weight residual 1.530 1.632 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" CB LEU A 34 " pdb=" CG LEU A 34 " ideal model delta sigma weight residual 1.530 1.630 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" CB PHE A 53 " pdb=" CG PHE A 53 " ideal model delta sigma weight residual 1.502 1.389 0.113 2.30e-02 1.89e+03 2.41e+01 ... (remaining 15827 not shown) Histogram of bond angle deviations from ideal: 97.56 - 104.91: 285 104.91 - 112.26: 8213 112.26 - 119.62: 6040 119.62 - 126.97: 6761 126.97 - 134.32: 236 Bond angle restraints: 21535 Sorted by residual: angle pdb=" C CYS A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta sigma weight residual 119.87 128.90 -9.03 1.04e+00 9.25e-01 7.53e+01 angle pdb=" C CYS D 205 " pdb=" N PRO D 206 " pdb=" CA PRO D 206 " ideal model delta sigma weight residual 119.56 127.68 -8.12 1.02e+00 9.61e-01 6.34e+01 angle pdb=" N PRO D 437 " pdb=" CA PRO D 437 " pdb=" C PRO D 437 " ideal model delta sigma weight residual 110.58 102.20 8.38 1.07e+00 8.73e-01 6.14e+01 angle pdb=" C GLY C 237 " pdb=" N PRO C 238 " pdb=" CA PRO C 238 " ideal model delta sigma weight residual 119.76 127.75 -7.99 1.03e+00 9.43e-01 6.02e+01 angle pdb=" C PRO A 437 " pdb=" N PRO A 438 " pdb=" CA PRO A 438 " ideal model delta sigma weight residual 120.03 127.67 -7.64 9.90e-01 1.02e+00 5.96e+01 ... (remaining 21530 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.32: 10314 21.32 - 42.64: 271 42.64 - 63.96: 69 63.96 - 85.28: 34 85.28 - 106.60: 18 Dihedral angle restraints: 10706 sinusoidal: 5279 harmonic: 5427 Sorted by residual: 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 93.00 159.34 -66.34 1 1.00e+01 1.00e-02 5.75e+01 dihedral pdb=" CA UNK H 27 " pdb=" C UNK H 27 " pdb=" N UNK H 28 " pdb=" CA UNK H 28 " ideal model delta harmonic sigma weight residual 180.00 -152.13 -27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA UNK L 11 " pdb=" C UNK L 11 " pdb=" N UNK L 12 " pdb=" CA UNK L 12 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 10703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1914 0.121 - 0.242: 511 0.242 - 0.363: 228 0.363 - 0.483: 108 0.483 - 0.604: 10 Chirality restraints: 2771 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.46e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.07e+02 chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.65e+02 ... (remaining 2768 not shown) Planarity restraints: 2678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG p 1 " -0.349 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG p 1 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG p 1 " -0.147 2.00e-02 2.50e+03 pdb=" N2 NAG p 1 " 0.531 2.00e-02 2.50e+03 pdb=" O7 NAG p 1 " -0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.346 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG K 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " 0.156 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.525 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 602 " 0.343 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" C7 NAG A 602 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A 602 " 0.066 2.00e-02 2.50e+03 pdb=" N2 NAG A 602 " -0.521 2.00e-02 2.50e+03 pdb=" O7 NAG A 602 " 0.194 2.00e-02 2.50e+03 ... (remaining 2675 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4815 2.85 - 3.36: 14777 3.36 - 3.88: 26103 3.88 - 4.39: 30469 4.39 - 4.90: 46672 Nonbonded interactions: 122836 Sorted by model distance: nonbonded pdb=" O3 NAG K 1 " pdb=" O7 NAG K 1 " model vdw 2.339 2.440 nonbonded pdb=" O PHE B 522 " pdb=" NE2 GLN B 540 " model vdw 2.366 2.520 nonbonded pdb=" OD1 ASP D 107 " pdb=" NZ LYS F 574 " model vdw 2.369 2.520 nonbonded pdb=" O3 NAG K 2 " pdb=" O7 NAG K 2 " model vdw 2.404 2.440 nonbonded pdb=" O3 NAG p 2 " pdb=" O7 NAG p 2 " model vdw 2.417 2.440 ... (remaining 122831 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 34 through 457 or resid 463 through 503 or resid 601 throu \ gh 604)) selection = (chain 'C' and (resid 34 through 184 or resid 189 through 397 or resid 411 throu \ gh 457 or resid 463 through 503 or resid 601 through 604)) selection = (chain 'D' and (resid 34 through 184 or resid 189 through 397 or resid 411 throu \ gh 503 or resid 601 through 604)) } ncs_group { reference = (chain 'B' and (resid 521 through 545 or resid 570 through 661 or resid 702)) selection = (chain 'E' and (resid 521 through 661 or resid 702)) selection = (chain 'F' and (resid 521 through 545 or resid 570 through 661 or resid 701)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' } ncs_group { reference = (chain 'H' and resid 7 through 108) selection = chain 'L' } ncs_group { reference = chain 'K' selection = chain 'Y' selection = chain 'h' } 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: 2.780 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: 0.030 Extract box with map and model: 10.700 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 45.380 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 : 0.022 0.148 15832 Z= 1.390 Angle : 1.762 10.885 21535 Z= 1.126 Chirality : 0.151 0.604 2771 Planarity : 0.018 0.299 2623 Dihedral : 11.788 106.603 7073 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.06 % 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: 0.57 (0.19), residues: 1620 helix: 0.16 (0.23), residues: 401 sheet: 0.79 (0.23), residues: 420 loop : 0.43 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.008 TRP A 479 HIS 0.013 0.002 HIS A 249 PHE 0.032 0.006 PHE A 353 TYR 0.048 0.010 TYR A 384 ARG 0.007 0.001 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 471 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LEU cc_start: 0.9102 (mt) cc_final: 0.8866 (mm) REVERT: A 201 ILE cc_start: 0.8935 (tp) cc_final: 0.8679 (pt) REVERT: A 434 MET cc_start: 0.9032 (tmm) cc_final: 0.8588 (tmm) REVERT: B 530 MET cc_start: 0.8868 (mtp) cc_final: 0.8326 (mtp) REVERT: B 536 THR cc_start: 0.8771 (p) cc_final: 0.8233 (t) REVERT: B 585 HIS cc_start: 0.9072 (m-70) cc_final: 0.8532 (m170) REVERT: B 586 TYR cc_start: 0.9290 (t80) cc_final: 0.8555 (t80) REVERT: B 588 ARG cc_start: 0.9439 (ttp80) cc_final: 0.8944 (ttm-80) REVERT: B 610 TRP cc_start: 0.8715 (t-100) cc_final: 0.8400 (t-100) REVERT: B 625 ASN cc_start: 0.9078 (m-40) cc_final: 0.8844 (t0) REVERT: B 634 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8687 (tp30) REVERT: B 635 ILE cc_start: 0.9558 (pt) cc_final: 0.8922 (pt) REVERT: B 659 ASP cc_start: 0.8977 (m-30) cc_final: 0.8475 (t0) REVERT: C 69 TRP cc_start: 0.7580 (m-90) cc_final: 0.7314 (m-90) REVERT: C 81 PRO cc_start: 0.8318 (Cg_endo) cc_final: 0.7748 (Cg_exo) REVERT: C 104 MET cc_start: 0.8879 (mtt) cc_final: 0.8604 (mmp) REVERT: C 191 TYR cc_start: 0.8446 (m-80) cc_final: 0.7798 (m-80) REVERT: C 199 SER cc_start: 0.8869 (p) cc_final: 0.8619 (m) REVERT: C 252 LYS cc_start: 0.9324 (mttt) cc_final: 0.9076 (mttm) REVERT: C 319 TYR cc_start: 0.8905 (p90) cc_final: 0.8416 (p90) REVERT: C 342 LEU cc_start: 0.9615 (mm) cc_final: 0.9389 (tp) REVERT: E 536 THR cc_start: 0.9361 (p) cc_final: 0.9061 (t) REVERT: E 575 GLN cc_start: 0.9242 (tt0) cc_final: 0.8874 (tp40) REVERT: E 584 GLU cc_start: 0.9130 (tt0) cc_final: 0.8890 (tm-30) REVERT: E 589 ASP cc_start: 0.9351 (m-30) cc_final: 0.9124 (p0) REVERT: E 591 GLN cc_start: 0.8821 (tt0) cc_final: 0.8254 (tp40) REVERT: E 607 ASN cc_start: 0.9436 (m-40) cc_final: 0.9179 (m-40) REVERT: E 620 SER cc_start: 0.7710 (m) cc_final: 0.7470 (p) REVERT: E 630 GLN cc_start: 0.9483 (mt0) cc_final: 0.9067 (mt0) REVERT: E 634 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8647 (mt-10) REVERT: E 659 ASP cc_start: 0.9114 (m-30) cc_final: 0.8868 (t0) REVERT: D 42 VAL cc_start: 0.9609 (t) cc_final: 0.9357 (p) REVERT: D 69 TRP cc_start: 0.8255 (m-90) cc_final: 0.7994 (m-90) REVERT: D 104 MET cc_start: 0.9104 (mmm) cc_final: 0.8546 (mmp) REVERT: D 117 LYS cc_start: 0.9236 (mttt) cc_final: 0.8846 (mmtp) REVERT: D 150 MET cc_start: 0.7974 (mtp) cc_final: 0.7425 (mtp) REVERT: D 199 SER cc_start: 0.8378 (p) cc_final: 0.8164 (m) REVERT: D 210 PHE cc_start: 0.8487 (m-80) cc_final: 0.8187 (m-80) REVERT: D 376 PHE cc_start: 0.8686 (p90) cc_final: 0.8188 (p90) REVERT: D 424 ILE cc_start: 0.9009 (mm) cc_final: 0.8553 (mp) REVERT: D 434 MET cc_start: 0.8914 (tmm) cc_final: 0.8208 (tmm) REVERT: F 530 MET cc_start: 0.9310 (mtp) cc_final: 0.8899 (mtp) REVERT: F 539 VAL cc_start: 0.9449 (p) cc_final: 0.9198 (t) REVERT: F 574 LYS cc_start: 0.9515 (mttt) cc_final: 0.8999 (tttm) REVERT: F 584 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8814 (tp30) REVERT: F 593 LEU cc_start: 0.9539 (mt) cc_final: 0.9293 (tp) REVERT: F 622 ILE cc_start: 0.8904 (mt) cc_final: 0.7966 (mm) REVERT: F 624 ASP cc_start: 0.8705 (m-30) cc_final: 0.8446 (t0) REVERT: F 626 MET cc_start: 0.8253 (tpp) cc_final: 0.6808 (tpp) outliers start: 0 outliers final: 0 residues processed: 471 average time/residue: 0.2983 time to fit residues: 198.2479 Evaluate side-chains 241 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 328 GLN A 422 GLN C 114 GLN C 422 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 HIS E 653 GLN D 114 GLN F 590 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15832 Z= 0.284 Angle : 0.788 9.947 21535 Z= 0.397 Chirality : 0.050 0.467 2771 Planarity : 0.005 0.050 2623 Dihedral : 9.490 79.315 3928 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.10 % Favored : 97.84 % Rotamer: Outliers : 0.20 % Allowed : 2.03 % Favored : 97.77 % 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: 0.36 (0.20), residues: 1620 helix: 0.87 (0.26), residues: 389 sheet: 0.69 (0.24), residues: 397 loop : -0.21 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 623 HIS 0.006 0.002 HIS A 85 PHE 0.022 0.003 PHE A 383 TYR 0.026 0.002 TYR D 217 ARG 0.007 0.001 ARG E 617 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 317 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8939 (t80) cc_final: 0.8476 (t80) REVERT: A 52 LEU cc_start: 0.9600 (mm) cc_final: 0.9003 (mm) REVERT: A 98 ASN cc_start: 0.9229 (t0) cc_final: 0.8981 (t0) REVERT: A 107 ASP cc_start: 0.8991 (t0) cc_final: 0.8571 (t0) REVERT: A 136 ASN cc_start: 0.8817 (m-40) cc_final: 0.8454 (p0) REVERT: A 161 MET cc_start: 0.8741 (tmm) cc_final: 0.8481 (tmm) REVERT: A 244 THR cc_start: 0.9109 (m) cc_final: 0.8629 (t) REVERT: A 384 TYR cc_start: 0.8430 (m-80) cc_final: 0.8214 (m-80) REVERT: A 424 ILE cc_start: 0.8720 (mm) cc_final: 0.7860 (mp) REVERT: A 426 MET cc_start: 0.8896 (ptt) cc_final: 0.8539 (ptt) REVERT: B 530 MET cc_start: 0.8603 (mtp) cc_final: 0.8369 (mtp) REVERT: B 536 THR cc_start: 0.8969 (p) cc_final: 0.8719 (t) REVERT: B 543 ASN cc_start: 0.9455 (m-40) cc_final: 0.9040 (m110) REVERT: B 584 GLU cc_start: 0.8705 (pp20) cc_final: 0.8178 (pp20) REVERT: B 585 HIS cc_start: 0.8938 (m-70) cc_final: 0.8323 (m-70) REVERT: B 586 TYR cc_start: 0.9126 (t80) cc_final: 0.8542 (t80) REVERT: B 588 ARG cc_start: 0.9493 (ttp80) cc_final: 0.8965 (ttm-80) REVERT: B 589 ASP cc_start: 0.9340 (m-30) cc_final: 0.9078 (m-30) REVERT: B 595 ILE cc_start: 0.9492 (pt) cc_final: 0.9242 (tt) REVERT: B 603 ILE cc_start: 0.8099 (pt) cc_final: 0.7688 (pt) REVERT: B 610 TRP cc_start: 0.8796 (t-100) cc_final: 0.8461 (t-100) REVERT: B 634 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8617 (tp30) REVERT: B 635 ILE cc_start: 0.9481 (pt) cc_final: 0.9243 (pt) REVERT: C 39 TYR cc_start: 0.7928 (m-80) cc_final: 0.7609 (m-10) REVERT: C 112 TRP cc_start: 0.9031 (t-100) cc_final: 0.8752 (t-100) REVERT: C 116 LEU cc_start: 0.9536 (tp) cc_final: 0.9235 (tp) REVERT: C 191 TYR cc_start: 0.8301 (m-80) cc_final: 0.7728 (m-80) REVERT: C 211 GLU cc_start: 0.8819 (tt0) cc_final: 0.8515 (tt0) REVERT: C 217 TYR cc_start: 0.7350 (m-80) cc_final: 0.6626 (m-80) REVERT: C 319 TYR cc_start: 0.9139 (p90) cc_final: 0.8339 (p90) REVERT: C 434 MET cc_start: 0.9045 (ttm) cc_final: 0.8732 (ttp) REVERT: C 477 ASP cc_start: 0.9521 (m-30) cc_final: 0.9295 (p0) REVERT: E 584 GLU cc_start: 0.9279 (tt0) cc_final: 0.8954 (tm-30) REVERT: E 589 ASP cc_start: 0.9303 (m-30) cc_final: 0.9058 (p0) REVERT: E 620 SER cc_start: 0.7755 (m) cc_final: 0.7447 (p) REVERT: E 648 GLU cc_start: 0.9435 (pt0) cc_final: 0.9049 (pt0) REVERT: E 654 GLU cc_start: 0.9101 (tp30) cc_final: 0.8712 (tp30) REVERT: E 659 ASP cc_start: 0.9220 (m-30) cc_final: 0.8968 (t0) REVERT: D 42 VAL cc_start: 0.9508 (t) cc_final: 0.9104 (p) REVERT: D 121 LYS cc_start: 0.9173 (pptt) cc_final: 0.8813 (ptmm) REVERT: D 154 LEU cc_start: 0.9581 (mt) cc_final: 0.9133 (tt) REVERT: D 180 ASP cc_start: 0.8559 (m-30) cc_final: 0.8213 (m-30) REVERT: D 210 PHE cc_start: 0.8423 (m-80) cc_final: 0.8218 (m-80) REVERT: D 376 PHE cc_start: 0.8834 (p90) cc_final: 0.8143 (p90) REVERT: D 383 PHE cc_start: 0.9166 (m-80) cc_final: 0.8807 (m-80) REVERT: F 522 PHE cc_start: 0.8883 (t80) cc_final: 0.8513 (t80) REVERT: F 622 ILE cc_start: 0.8664 (mt) cc_final: 0.7880 (mm) REVERT: F 624 ASP cc_start: 0.8671 (m-30) cc_final: 0.8430 (t0) REVERT: F 633 LYS cc_start: 0.9143 (mmmt) cc_final: 0.8841 (mmmt) REVERT: F 639 THR cc_start: 0.9288 (m) cc_final: 0.9044 (m) REVERT: F 654 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7177 (mm-30) outliers start: 3 outliers final: 1 residues processed: 318 average time/residue: 0.2931 time to fit residues: 136.1774 Evaluate side-chains 233 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 167 optimal weight: 0.0050 chunk 180 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 overall best weight: 3.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN E 653 GLN D 328 GLN F 590 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 15832 Z= 0.322 Angle : 0.750 7.706 21535 Z= 0.380 Chirality : 0.047 0.491 2771 Planarity : 0.005 0.045 2623 Dihedral : 8.700 71.272 3928 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.59 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % 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: 0.05 (0.20), residues: 1620 helix: 0.77 (0.27), residues: 388 sheet: 0.57 (0.24), residues: 406 loop : -0.54 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 623 HIS 0.008 0.002 HIS A 85 PHE 0.029 0.003 PHE A 391 TYR 0.028 0.002 TYR F 643 ARG 0.006 0.001 ARG C 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9532 (mm) cc_final: 0.9263 (mm) REVERT: A 122 LEU cc_start: 0.9317 (mt) cc_final: 0.9039 (mm) REVERT: A 136 ASN cc_start: 0.8856 (m-40) cc_final: 0.8468 (p0) REVERT: A 161 MET cc_start: 0.8805 (tmm) cc_final: 0.8562 (tmm) REVERT: A 244 THR cc_start: 0.9235 (m) cc_final: 0.8683 (t) REVERT: A 384 TYR cc_start: 0.8583 (m-80) cc_final: 0.8299 (m-80) REVERT: A 434 MET cc_start: 0.8977 (tmm) cc_final: 0.8733 (tmm) REVERT: B 536 THR cc_start: 0.9102 (p) cc_final: 0.8894 (t) REVERT: B 543 ASN cc_start: 0.9563 (m-40) cc_final: 0.9034 (m110) REVERT: B 584 GLU cc_start: 0.8772 (pp20) cc_final: 0.8174 (pp20) REVERT: B 585 HIS cc_start: 0.8653 (m90) cc_final: 0.8126 (m-70) REVERT: B 588 ARG cc_start: 0.9523 (ttp80) cc_final: 0.8967 (ttm-80) REVERT: B 591 GLN cc_start: 0.9342 (tt0) cc_final: 0.9082 (tm-30) REVERT: B 595 ILE cc_start: 0.9565 (pt) cc_final: 0.9219 (tt) REVERT: B 603 ILE cc_start: 0.8234 (pt) cc_final: 0.7679 (pt) REVERT: B 610 TRP cc_start: 0.8972 (t-100) cc_final: 0.8755 (t-100) REVERT: B 622 ILE cc_start: 0.9288 (mp) cc_final: 0.8735 (mp) REVERT: B 634 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8739 (tp30) REVERT: B 654 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8597 (mt-10) REVERT: C 39 TYR cc_start: 0.8083 (m-80) cc_final: 0.7605 (m-10) REVERT: C 40 TYR cc_start: 0.9215 (t80) cc_final: 0.8924 (t80) REVERT: C 116 LEU cc_start: 0.9646 (tp) cc_final: 0.9095 (tp) REVERT: C 191 TYR cc_start: 0.8444 (m-80) cc_final: 0.7952 (m-80) REVERT: C 319 TYR cc_start: 0.9219 (p90) cc_final: 0.8490 (p90) REVERT: C 426 MET cc_start: 0.9320 (tpp) cc_final: 0.8982 (tpp) REVERT: C 434 MET cc_start: 0.9058 (ttm) cc_final: 0.8248 (ttp) REVERT: E 584 GLU cc_start: 0.9353 (tt0) cc_final: 0.9015 (tm-30) REVERT: E 589 ASP cc_start: 0.9390 (m-30) cc_final: 0.9081 (p0) REVERT: E 603 ILE cc_start: 0.9059 (mt) cc_final: 0.8847 (mt) REVERT: E 620 SER cc_start: 0.8234 (m) cc_final: 0.7913 (p) REVERT: E 654 GLU cc_start: 0.9087 (tp30) cc_final: 0.8650 (tp30) REVERT: D 117 LYS cc_start: 0.9142 (mtmm) cc_final: 0.8843 (mtmm) REVERT: D 121 LYS cc_start: 0.9222 (pptt) cc_final: 0.8996 (pttp) REVERT: D 154 LEU cc_start: 0.9624 (mt) cc_final: 0.9224 (tt) REVERT: D 210 PHE cc_start: 0.8563 (m-80) cc_final: 0.8323 (m-80) REVERT: D 376 PHE cc_start: 0.8957 (p90) cc_final: 0.8254 (p90) REVERT: D 383 PHE cc_start: 0.9303 (m-80) cc_final: 0.8761 (m-80) REVERT: D 424 ILE cc_start: 0.9060 (tp) cc_final: 0.8533 (tp) REVERT: F 522 PHE cc_start: 0.8997 (t80) cc_final: 0.8740 (t80) REVERT: F 539 VAL cc_start: 0.9643 (t) cc_final: 0.9432 (p) REVERT: F 624 ASP cc_start: 0.8601 (m-30) cc_final: 0.8326 (t0) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2718 time to fit residues: 108.8023 Evaluate side-chains 199 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 50.0000 chunk 79 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 159 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 GLN D 170 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15832 Z= 0.293 Angle : 0.694 7.115 21535 Z= 0.349 Chirality : 0.048 0.744 2771 Planarity : 0.004 0.046 2623 Dihedral : 8.343 61.404 3928 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.30 % Rotamer: Outliers : 0.07 % Allowed : 1.55 % Favored : 98.38 % 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: -0.20 (0.20), residues: 1620 helix: 0.68 (0.27), residues: 387 sheet: 0.33 (0.24), residues: 444 loop : -0.77 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 112 HIS 0.006 0.001 HIS A 85 PHE 0.018 0.002 PHE C 382 TYR 0.025 0.002 TYR A 217 ARG 0.006 0.001 ARG D 419 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9463 (mm) cc_final: 0.9184 (mm) REVERT: A 136 ASN cc_start: 0.8890 (m-40) cc_final: 0.8485 (p0) REVERT: A 244 THR cc_start: 0.9120 (m) cc_final: 0.8692 (t) REVERT: A 384 TYR cc_start: 0.8680 (m-80) cc_final: 0.8318 (m-80) REVERT: B 538 THR cc_start: 0.9139 (p) cc_final: 0.8899 (p) REVERT: B 543 ASN cc_start: 0.9559 (m-40) cc_final: 0.9077 (m110) REVERT: B 584 GLU cc_start: 0.8839 (pp20) cc_final: 0.8210 (pp20) REVERT: B 585 HIS cc_start: 0.8887 (m90) cc_final: 0.8318 (m-70) REVERT: B 588 ARG cc_start: 0.9493 (ttp80) cc_final: 0.8905 (ttm-80) REVERT: B 591 GLN cc_start: 0.9335 (tt0) cc_final: 0.9059 (tm-30) REVERT: B 595 ILE cc_start: 0.9554 (pt) cc_final: 0.9210 (tt) REVERT: B 622 ILE cc_start: 0.9277 (mp) cc_final: 0.9009 (mp) REVERT: B 634 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8708 (tp30) REVERT: B 651 ASN cc_start: 0.9045 (t0) cc_final: 0.8733 (t0) REVERT: B 654 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8288 (mt-10) REVERT: C 39 TYR cc_start: 0.8074 (m-80) cc_final: 0.7455 (m-80) REVERT: C 40 TYR cc_start: 0.9193 (t80) cc_final: 0.8847 (t80) REVERT: C 116 LEU cc_start: 0.9656 (tp) cc_final: 0.9182 (tp) REVERT: C 191 TYR cc_start: 0.8513 (m-80) cc_final: 0.7980 (m-80) REVERT: C 319 TYR cc_start: 0.9162 (p90) cc_final: 0.8373 (p90) REVERT: C 434 MET cc_start: 0.9069 (ttm) cc_final: 0.8260 (ttm) REVERT: E 571 TRP cc_start: 0.8952 (m100) cc_final: 0.8425 (m100) REVERT: E 575 GLN cc_start: 0.9272 (tt0) cc_final: 0.8836 (tp40) REVERT: E 584 GLU cc_start: 0.9312 (tt0) cc_final: 0.9002 (tm-30) REVERT: E 589 ASP cc_start: 0.9359 (m-30) cc_final: 0.9063 (p0) REVERT: E 603 ILE cc_start: 0.9090 (mt) cc_final: 0.8806 (mt) REVERT: E 632 ASP cc_start: 0.9109 (t0) cc_final: 0.8817 (p0) REVERT: E 654 GLU cc_start: 0.9099 (tp30) cc_final: 0.8799 (tp30) REVERT: E 655 LYS cc_start: 0.9514 (tptp) cc_final: 0.8985 (tppt) REVERT: D 121 LYS cc_start: 0.9271 (pptt) cc_final: 0.8905 (ptmm) REVERT: D 129 LEU cc_start: 0.9514 (mt) cc_final: 0.9172 (mp) REVERT: D 154 LEU cc_start: 0.9575 (mt) cc_final: 0.9171 (tp) REVERT: D 210 PHE cc_start: 0.8521 (m-80) cc_final: 0.8194 (m-80) REVERT: D 376 PHE cc_start: 0.8937 (p90) cc_final: 0.8134 (p90) REVERT: D 383 PHE cc_start: 0.9262 (m-80) cc_final: 0.8816 (m-80) REVERT: D 424 ILE cc_start: 0.9220 (tp) cc_final: 0.8534 (tp) REVERT: F 574 LYS cc_start: 0.9216 (ptmm) cc_final: 0.8960 (ptmm) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.2705 time to fit residues: 101.0561 Evaluate side-chains 180 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 2 optimal weight: 30.0000 chunk 132 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 15832 Z= 0.377 Angle : 0.773 7.856 21535 Z= 0.387 Chirality : 0.048 0.563 2771 Planarity : 0.005 0.054 2623 Dihedral : 8.611 57.756 3928 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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: -0.67 (0.20), residues: 1620 helix: 0.40 (0.27), residues: 370 sheet: -0.08 (0.23), residues: 460 loop : -1.03 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 427 HIS 0.007 0.002 HIS A 85 PHE 0.023 0.003 PHE C 361 TYR 0.040 0.002 TYR C 217 ARG 0.005 0.001 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9414 (mm) cc_final: 0.9174 (mm) REVERT: A 98 ASN cc_start: 0.9388 (t0) cc_final: 0.9181 (t0) REVERT: A 122 LEU cc_start: 0.9381 (mt) cc_final: 0.9063 (mm) REVERT: A 136 ASN cc_start: 0.8944 (m-40) cc_final: 0.8578 (p0) REVERT: A 384 TYR cc_start: 0.8721 (m-80) cc_final: 0.8330 (m-80) REVERT: B 543 ASN cc_start: 0.9516 (m-40) cc_final: 0.9063 (m110) REVERT: B 585 HIS cc_start: 0.8831 (m90) cc_final: 0.8359 (m90) REVERT: B 586 TYR cc_start: 0.8875 (t80) cc_final: 0.8533 (t80) REVERT: B 588 ARG cc_start: 0.9513 (ttp80) cc_final: 0.8898 (ttm-80) REVERT: B 591 GLN cc_start: 0.9352 (tt0) cc_final: 0.9068 (tm-30) REVERT: B 595 ILE cc_start: 0.9572 (pt) cc_final: 0.9243 (tt) REVERT: B 603 ILE cc_start: 0.8323 (pt) cc_final: 0.7920 (pt) REVERT: B 634 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8706 (tp30) REVERT: B 651 ASN cc_start: 0.9119 (t0) cc_final: 0.8793 (t0) REVERT: B 654 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8266 (mt-10) REVERT: C 39 TYR cc_start: 0.8174 (m-80) cc_final: 0.7391 (m-10) REVERT: C 40 TYR cc_start: 0.9270 (t80) cc_final: 0.8928 (t80) REVERT: C 100 MET cc_start: 0.9042 (mtm) cc_final: 0.8791 (ttm) REVERT: C 116 LEU cc_start: 0.9640 (tp) cc_final: 0.8976 (tp) REVERT: C 191 TYR cc_start: 0.8606 (m-80) cc_final: 0.8141 (m-80) REVERT: C 319 TYR cc_start: 0.9184 (p90) cc_final: 0.8391 (p90) REVERT: C 434 MET cc_start: 0.9099 (ttm) cc_final: 0.8179 (ttp) REVERT: E 571 TRP cc_start: 0.8750 (m100) cc_final: 0.8271 (m100) REVERT: E 575 GLN cc_start: 0.9322 (tt0) cc_final: 0.8859 (tp40) REVERT: E 584 GLU cc_start: 0.9348 (tt0) cc_final: 0.9085 (tm-30) REVERT: E 589 ASP cc_start: 0.9378 (m-30) cc_final: 0.9119 (p0) REVERT: E 603 ILE cc_start: 0.9158 (mt) cc_final: 0.8866 (mt) REVERT: E 632 ASP cc_start: 0.9084 (t0) cc_final: 0.8813 (p0) REVERT: E 653 GLN cc_start: 0.9526 (tt0) cc_final: 0.9287 (tt0) REVERT: E 654 GLU cc_start: 0.9152 (tp30) cc_final: 0.8904 (tp30) REVERT: E 655 LYS cc_start: 0.9568 (tptp) cc_final: 0.8991 (tppt) REVERT: E 658 GLN cc_start: 0.9303 (tm-30) cc_final: 0.8857 (tm-30) REVERT: D 121 LYS cc_start: 0.9299 (pptt) cc_final: 0.8953 (ptmm) REVERT: D 376 PHE cc_start: 0.8922 (p90) cc_final: 0.8179 (p90) REVERT: D 383 PHE cc_start: 0.9260 (m-80) cc_final: 0.8852 (m-80) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2761 time to fit residues: 92.5757 Evaluate side-chains 169 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN C 195 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN D 377 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15832 Z= 0.215 Angle : 0.648 9.459 21535 Z= 0.323 Chirality : 0.047 0.656 2771 Planarity : 0.004 0.056 2623 Dihedral : 8.089 58.477 3928 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.98 % Rotamer: Outliers : 0.07 % Allowed : 1.42 % Favored : 98.51 % 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: -0.52 (0.21), residues: 1620 helix: 0.49 (0.28), residues: 381 sheet: -0.00 (0.24), residues: 456 loop : -0.92 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 571 HIS 0.008 0.001 HIS A 105 PHE 0.015 0.002 PHE C 382 TYR 0.036 0.002 TYR D 217 ARG 0.007 0.000 ARG F 617 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9477 (mm) cc_final: 0.9255 (mm) REVERT: A 98 ASN cc_start: 0.9401 (t0) cc_final: 0.9144 (t0) REVERT: A 122 LEU cc_start: 0.9371 (mt) cc_final: 0.9054 (mm) REVERT: A 136 ASN cc_start: 0.8927 (m-40) cc_final: 0.8559 (p0) REVERT: A 177 TYR cc_start: 0.8507 (m-10) cc_final: 0.8298 (m-80) REVERT: A 217 TYR cc_start: 0.7493 (m-80) cc_final: 0.7135 (m-80) REVERT: A 244 THR cc_start: 0.9159 (m) cc_final: 0.8678 (t) REVERT: B 538 THR cc_start: 0.9164 (p) cc_final: 0.8952 (p) REVERT: B 543 ASN cc_start: 0.9549 (m-40) cc_final: 0.9309 (m110) REVERT: B 584 GLU cc_start: 0.8857 (pp20) cc_final: 0.8221 (pp20) REVERT: B 585 HIS cc_start: 0.8779 (m90) cc_final: 0.8147 (m-70) REVERT: B 588 ARG cc_start: 0.9528 (ttp80) cc_final: 0.8874 (ttm-80) REVERT: B 591 GLN cc_start: 0.9322 (tt0) cc_final: 0.9053 (tm-30) REVERT: B 595 ILE cc_start: 0.9577 (pt) cc_final: 0.9262 (tt) REVERT: B 603 ILE cc_start: 0.8407 (pt) cc_final: 0.7844 (pt) REVERT: B 634 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8666 (tp30) REVERT: B 651 ASN cc_start: 0.9076 (t0) cc_final: 0.8767 (t0) REVERT: B 654 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8448 (mt-10) REVERT: C 39 TYR cc_start: 0.8079 (m-80) cc_final: 0.7447 (m-80) REVERT: C 40 TYR cc_start: 0.9213 (t80) cc_final: 0.8829 (t80) REVERT: C 45 TRP cc_start: 0.8391 (p90) cc_final: 0.8066 (p90) REVERT: C 106 GLU cc_start: 0.9520 (mt-10) cc_final: 0.9285 (mp0) REVERT: C 116 LEU cc_start: 0.9653 (tp) cc_final: 0.8990 (tp) REVERT: C 191 TYR cc_start: 0.8534 (m-80) cc_final: 0.8005 (m-80) REVERT: C 319 TYR cc_start: 0.9196 (p90) cc_final: 0.8401 (p90) REVERT: C 434 MET cc_start: 0.9074 (ttm) cc_final: 0.8092 (ttp) REVERT: E 575 GLN cc_start: 0.9295 (tt0) cc_final: 0.8823 (tp40) REVERT: E 584 GLU cc_start: 0.9316 (tt0) cc_final: 0.9053 (tm-30) REVERT: E 589 ASP cc_start: 0.9346 (m-30) cc_final: 0.9049 (p0) REVERT: E 603 ILE cc_start: 0.9099 (mt) cc_final: 0.8816 (mt) REVERT: E 632 ASP cc_start: 0.9069 (t0) cc_final: 0.8754 (p0) REVERT: E 653 GLN cc_start: 0.9535 (tt0) cc_final: 0.9296 (tt0) REVERT: E 654 GLU cc_start: 0.9108 (tp30) cc_final: 0.8846 (tp30) REVERT: E 655 LYS cc_start: 0.9434 (tptp) cc_final: 0.9226 (tptm) REVERT: D 121 LYS cc_start: 0.9244 (pptt) cc_final: 0.9022 (pptt) REVERT: D 123 THR cc_start: 0.9285 (m) cc_final: 0.9031 (m) REVERT: D 376 PHE cc_start: 0.8919 (p90) cc_final: 0.8167 (p90) REVERT: D 383 PHE cc_start: 0.9084 (m-80) cc_final: 0.8678 (m-80) REVERT: D 424 ILE cc_start: 0.9088 (tp) cc_final: 0.8543 (tp) REVERT: F 539 VAL cc_start: 0.9576 (t) cc_final: 0.9280 (t) outliers start: 1 outliers final: 0 residues processed: 246 average time/residue: 0.2789 time to fit residues: 100.7431 Evaluate side-chains 188 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 177 optimal weight: 0.9980 chunk 110 optimal weight: 0.1980 chunk 108 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15832 Z= 0.179 Angle : 0.606 7.430 21535 Z= 0.303 Chirality : 0.045 0.616 2771 Planarity : 0.004 0.048 2623 Dihedral : 7.575 58.205 3928 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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: -0.44 (0.21), residues: 1620 helix: 0.84 (0.28), residues: 375 sheet: 0.00 (0.23), residues: 470 loop : -1.02 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 69 HIS 0.008 0.001 HIS A 105 PHE 0.013 0.001 PHE C 382 TYR 0.016 0.001 TYR C 217 ARG 0.009 0.000 ARG F 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9434 (mm) cc_final: 0.9207 (mm) REVERT: A 109 ILE cc_start: 0.9632 (mt) cc_final: 0.9408 (tp) REVERT: A 122 LEU cc_start: 0.9378 (mt) cc_final: 0.9035 (mm) REVERT: A 136 ASN cc_start: 0.8959 (m-40) cc_final: 0.8575 (p0) REVERT: A 217 TYR cc_start: 0.7455 (m-80) cc_final: 0.6882 (m-80) REVERT: A 244 THR cc_start: 0.9155 (m) cc_final: 0.8709 (t) REVERT: A 427 TRP cc_start: 0.8182 (m100) cc_final: 0.7706 (m100) REVERT: B 538 THR cc_start: 0.9202 (p) cc_final: 0.8385 (p) REVERT: B 543 ASN cc_start: 0.9449 (m-40) cc_final: 0.9022 (m110) REVERT: B 584 GLU cc_start: 0.8888 (pp20) cc_final: 0.8223 (pp20) REVERT: B 585 HIS cc_start: 0.8772 (m90) cc_final: 0.8130 (m-70) REVERT: B 588 ARG cc_start: 0.9514 (ttp80) cc_final: 0.8883 (ttm-80) REVERT: B 591 GLN cc_start: 0.9286 (tt0) cc_final: 0.9017 (tm-30) REVERT: B 595 ILE cc_start: 0.9560 (pt) cc_final: 0.9241 (tt) REVERT: B 603 ILE cc_start: 0.8369 (pt) cc_final: 0.7772 (pt) REVERT: B 634 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8666 (tp30) REVERT: B 651 ASN cc_start: 0.9055 (t0) cc_final: 0.8808 (t0) REVERT: B 654 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8471 (mt-10) REVERT: C 39 TYR cc_start: 0.8023 (m-80) cc_final: 0.7408 (m-80) REVERT: C 40 TYR cc_start: 0.9266 (t80) cc_final: 0.8705 (t80) REVERT: C 45 TRP cc_start: 0.8380 (p90) cc_final: 0.8093 (p90) REVERT: C 106 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9210 (mp0) REVERT: C 116 LEU cc_start: 0.9655 (tp) cc_final: 0.8982 (tp) REVERT: C 191 TYR cc_start: 0.8473 (m-80) cc_final: 0.7899 (m-80) REVERT: C 319 TYR cc_start: 0.9207 (p90) cc_final: 0.8439 (p90) REVERT: C 434 MET cc_start: 0.8976 (ttm) cc_final: 0.8000 (ttp) REVERT: E 542 ARG cc_start: 0.8282 (ptp-110) cc_final: 0.7644 (ptp-170) REVERT: E 575 GLN cc_start: 0.9284 (tt0) cc_final: 0.8852 (tp40) REVERT: E 584 GLU cc_start: 0.9337 (tt0) cc_final: 0.9042 (tm-30) REVERT: E 589 ASP cc_start: 0.9306 (m-30) cc_final: 0.9004 (p0) REVERT: E 603 ILE cc_start: 0.9082 (mt) cc_final: 0.8788 (mt) REVERT: E 632 ASP cc_start: 0.9024 (t0) cc_final: 0.8725 (p0) REVERT: E 653 GLN cc_start: 0.9535 (tt0) cc_final: 0.9333 (tt0) REVERT: D 256 SER cc_start: 0.7925 (p) cc_final: 0.7333 (t) REVERT: D 376 PHE cc_start: 0.8932 (p90) cc_final: 0.8199 (p90) REVERT: D 383 PHE cc_start: 0.9008 (m-80) cc_final: 0.8629 (m-80) REVERT: D 424 ILE cc_start: 0.9069 (tp) cc_final: 0.8471 (tp) REVERT: F 574 LYS cc_start: 0.9240 (ptmm) cc_final: 0.8983 (ptmm) REVERT: F 633 LYS cc_start: 0.9350 (mmmm) cc_final: 0.9145 (mmmm) REVERT: F 656 ASN cc_start: 0.9144 (m110) cc_final: 0.8940 (m110) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.2551 time to fit residues: 92.2889 Evaluate side-chains 186 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 112 optimal weight: 0.0470 chunk 120 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 139 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 overall best weight: 4.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.6004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 15832 Z= 0.357 Angle : 0.752 10.084 21535 Z= 0.371 Chirality : 0.048 0.654 2771 Planarity : 0.005 0.056 2623 Dihedral : 8.197 57.806 3928 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: 1620 helix: 0.33 (0.27), residues: 372 sheet: -0.22 (0.24), residues: 459 loop : -1.17 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 427 HIS 0.009 0.001 HIS A 105 PHE 0.023 0.002 PHE B 522 TYR 0.024 0.002 TYR A 39 ARG 0.007 0.001 ARG F 542 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8718 (tpp) cc_final: 0.8517 (tpt) REVERT: A 109 ILE cc_start: 0.9721 (mt) cc_final: 0.9409 (tp) REVERT: A 217 TYR cc_start: 0.7616 (m-80) cc_final: 0.6883 (m-80) REVERT: A 427 TRP cc_start: 0.8384 (m100) cc_final: 0.8008 (m100) REVERT: B 530 MET cc_start: 0.8368 (ppp) cc_final: 0.8059 (ppp) REVERT: B 538 THR cc_start: 0.9099 (p) cc_final: 0.8886 (p) REVERT: B 543 ASN cc_start: 0.9528 (m-40) cc_final: 0.9166 (m110) REVERT: B 586 TYR cc_start: 0.9156 (t80) cc_final: 0.8573 (t80) REVERT: B 588 ARG cc_start: 0.9548 (ttp80) cc_final: 0.8851 (ttm-80) REVERT: B 591 GLN cc_start: 0.9386 (tt0) cc_final: 0.9076 (tm-30) REVERT: B 595 ILE cc_start: 0.9603 (pt) cc_final: 0.9284 (tt) REVERT: B 622 ILE cc_start: 0.9517 (mp) cc_final: 0.9163 (mp) REVERT: B 626 MET cc_start: 0.9211 (tpp) cc_final: 0.8983 (tpp) REVERT: B 634 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8569 (tp30) REVERT: B 651 ASN cc_start: 0.9065 (t0) cc_final: 0.8723 (t0) REVERT: B 654 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8343 (mt-10) REVERT: C 39 TYR cc_start: 0.8184 (m-80) cc_final: 0.7453 (m-10) REVERT: C 40 TYR cc_start: 0.9293 (t80) cc_final: 0.8888 (t80) REVERT: C 45 TRP cc_start: 0.8552 (p90) cc_final: 0.8264 (p90) REVERT: C 100 MET cc_start: 0.9189 (mtm) cc_final: 0.8987 (mtm) REVERT: C 106 GLU cc_start: 0.9478 (mt-10) cc_final: 0.9185 (mp0) REVERT: C 116 LEU cc_start: 0.9663 (tp) cc_final: 0.9191 (tp) REVERT: C 191 TYR cc_start: 0.8584 (m-80) cc_final: 0.7991 (m-80) REVERT: C 252 LYS cc_start: 0.9410 (mmtp) cc_final: 0.9066 (tppt) REVERT: C 319 TYR cc_start: 0.9228 (p90) cc_final: 0.8468 (p90) REVERT: C 434 MET cc_start: 0.9083 (ttm) cc_final: 0.8196 (ttm) REVERT: E 542 ARG cc_start: 0.8324 (ptp-110) cc_final: 0.7512 (ptp-170) REVERT: E 575 GLN cc_start: 0.9367 (tt0) cc_final: 0.8963 (tp40) REVERT: E 584 GLU cc_start: 0.9448 (tt0) cc_final: 0.9048 (tm-30) REVERT: E 603 ILE cc_start: 0.9189 (mt) cc_final: 0.8968 (mt) REVERT: E 632 ASP cc_start: 0.9114 (t0) cc_final: 0.8896 (p0) REVERT: E 655 LYS cc_start: 0.9520 (tptp) cc_final: 0.9184 (tppt) REVERT: E 658 GLN cc_start: 0.9361 (tm-30) cc_final: 0.8958 (tm-30) REVERT: D 256 SER cc_start: 0.8152 (p) cc_final: 0.7417 (t) REVERT: D 376 PHE cc_start: 0.8994 (p90) cc_final: 0.8286 (p90) REVERT: D 383 PHE cc_start: 0.9140 (m-80) cc_final: 0.8768 (m-80) REVERT: D 424 ILE cc_start: 0.9199 (tp) cc_final: 0.8943 (mp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2620 time to fit residues: 83.9229 Evaluate side-chains 161 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.9990 chunk 155 optimal weight: 0.5980 chunk 165 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 HIS ** E 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 625 ASN D 99 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.6054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15832 Z= 0.168 Angle : 0.625 8.830 21535 Z= 0.309 Chirality : 0.046 0.572 2771 Planarity : 0.004 0.048 2623 Dihedral : 7.385 58.607 3928 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -0.61 (0.21), residues: 1620 helix: 0.51 (0.28), residues: 373 sheet: -0.07 (0.23), residues: 487 loop : -1.04 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 571 HIS 0.008 0.001 HIS A 105 PHE 0.012 0.001 PHE C 376 TYR 0.025 0.002 TYR A 39 ARG 0.005 0.000 ARG F 542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9460 (mm) cc_final: 0.9187 (mm) REVERT: A 109 ILE cc_start: 0.9719 (mt) cc_final: 0.9385 (tp) REVERT: A 217 TYR cc_start: 0.7508 (m-80) cc_final: 0.6867 (m-80) REVERT: A 244 THR cc_start: 0.9108 (m) cc_final: 0.8652 (t) REVERT: B 530 MET cc_start: 0.8239 (ppp) cc_final: 0.7991 (ppp) REVERT: B 542 ARG cc_start: 0.8949 (ptt90) cc_final: 0.8685 (ptt-90) REVERT: B 543 ASN cc_start: 0.9475 (m-40) cc_final: 0.8068 (t0) REVERT: B 584 GLU cc_start: 0.8775 (pp20) cc_final: 0.8164 (pp20) REVERT: B 585 HIS cc_start: 0.8795 (m90) cc_final: 0.8174 (m-70) REVERT: B 586 TYR cc_start: 0.8991 (t80) cc_final: 0.8577 (t80) REVERT: B 588 ARG cc_start: 0.9516 (ttp80) cc_final: 0.8837 (ttm-80) REVERT: B 591 GLN cc_start: 0.9294 (tt0) cc_final: 0.9003 (tm-30) REVERT: B 595 ILE cc_start: 0.9585 (pt) cc_final: 0.9266 (tt) REVERT: B 622 ILE cc_start: 0.9396 (mp) cc_final: 0.9068 (mp) REVERT: B 629 LEU cc_start: 0.9089 (pp) cc_final: 0.8695 (tp) REVERT: B 634 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8628 (tp30) REVERT: B 651 ASN cc_start: 0.9081 (t0) cc_final: 0.8793 (t0) REVERT: B 654 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8425 (mt-10) REVERT: C 39 TYR cc_start: 0.8049 (m-80) cc_final: 0.7352 (m-80) REVERT: C 45 TRP cc_start: 0.8289 (p90) cc_final: 0.8081 (p90) REVERT: C 106 GLU cc_start: 0.9349 (mt-10) cc_final: 0.9036 (mp0) REVERT: C 116 LEU cc_start: 0.9653 (tp) cc_final: 0.8935 (tp) REVERT: C 191 TYR cc_start: 0.8495 (m-80) cc_final: 0.7849 (m-80) REVERT: C 319 TYR cc_start: 0.9229 (p90) cc_final: 0.8472 (p90) REVERT: C 434 MET cc_start: 0.8944 (ttm) cc_final: 0.7984 (ttp) REVERT: E 575 GLN cc_start: 0.9295 (tt0) cc_final: 0.8945 (tp40) REVERT: E 584 GLU cc_start: 0.9411 (tt0) cc_final: 0.9095 (tm-30) REVERT: E 603 ILE cc_start: 0.9089 (mt) cc_final: 0.8846 (mt) REVERT: E 632 ASP cc_start: 0.9007 (t0) cc_final: 0.8683 (p0) REVERT: D 104 MET cc_start: 0.8932 (mmp) cc_final: 0.8685 (mmp) REVERT: D 256 SER cc_start: 0.7890 (p) cc_final: 0.7369 (t) REVERT: D 376 PHE cc_start: 0.8908 (p90) cc_final: 0.8387 (p90) REVERT: D 383 PHE cc_start: 0.8910 (m-80) cc_final: 0.8558 (m-80) REVERT: D 424 ILE cc_start: 0.9125 (tp) cc_final: 0.8866 (tp) REVERT: F 537 LEU cc_start: 0.9342 (mt) cc_final: 0.8930 (mt) REVERT: F 539 VAL cc_start: 0.9604 (t) cc_final: 0.9351 (p) REVERT: F 574 LYS cc_start: 0.9234 (ptmm) cc_final: 0.9026 (ptmm) REVERT: F 581 LEU cc_start: 0.9277 (mm) cc_final: 0.8984 (tp) REVERT: F 656 ASN cc_start: 0.9118 (m110) cc_final: 0.8910 (m110) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2660 time to fit residues: 91.5277 Evaluate side-chains 180 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 168 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 15 optimal weight: 30.0000 chunk 112 optimal weight: 0.0980 chunk 89 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 ASN D 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 15832 Z= 0.383 Angle : 0.780 7.480 21535 Z= 0.385 Chirality : 0.049 0.628 2771 Planarity : 0.005 0.047 2623 Dihedral : 8.105 58.161 3928 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: -1.05 (0.20), residues: 1620 helix: -0.02 (0.27), residues: 369 sheet: -0.27 (0.24), residues: 456 loop : -1.24 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP A 427 HIS 0.008 0.002 HIS A 105 PHE 0.026 0.003 PHE B 522 TYR 0.033 0.002 TYR D 217 ARG 0.005 0.001 ARG F 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.7820 (m-80) cc_final: 0.7392 (m-80) REVERT: B 585 HIS cc_start: 0.8832 (m90) cc_final: 0.8335 (m90) REVERT: B 586 TYR cc_start: 0.9104 (t80) cc_final: 0.8561 (t80) REVERT: B 588 ARG cc_start: 0.9543 (ttp80) cc_final: 0.8906 (ttm-80) REVERT: B 591 GLN cc_start: 0.9384 (tt0) cc_final: 0.9091 (tm-30) REVERT: B 595 ILE cc_start: 0.9607 (pt) cc_final: 0.9297 (tt) REVERT: B 634 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8680 (tp30) REVERT: B 651 ASN cc_start: 0.9062 (t0) cc_final: 0.8761 (t0) REVERT: B 654 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8361 (mt-10) REVERT: C 39 TYR cc_start: 0.8236 (m-80) cc_final: 0.7454 (m-10) REVERT: C 45 TRP cc_start: 0.8597 (p90) cc_final: 0.8294 (p90) REVERT: C 106 GLU cc_start: 0.9497 (mt-10) cc_final: 0.9215 (mp0) REVERT: C 116 LEU cc_start: 0.9662 (tp) cc_final: 0.9164 (tp) REVERT: C 191 TYR cc_start: 0.8626 (m-80) cc_final: 0.7980 (m-80) REVERT: C 319 TYR cc_start: 0.9260 (p90) cc_final: 0.8552 (p90) REVERT: C 434 MET cc_start: 0.9110 (ttm) cc_final: 0.8194 (ttm) REVERT: E 584 GLU cc_start: 0.9457 (tt0) cc_final: 0.9048 (tm-30) REVERT: E 632 ASP cc_start: 0.9175 (t0) cc_final: 0.8905 (p0) REVERT: E 655 LYS cc_start: 0.9502 (tptp) cc_final: 0.9259 (tppt) REVERT: E 658 GLN cc_start: 0.9430 (tm-30) cc_final: 0.9039 (tm-30) REVERT: D 256 SER cc_start: 0.8228 (p) cc_final: 0.7322 (t) REVERT: D 376 PHE cc_start: 0.9077 (p90) cc_final: 0.8357 (p90) REVERT: D 383 PHE cc_start: 0.9132 (m-80) cc_final: 0.8729 (m-80) REVERT: F 574 LYS cc_start: 0.9089 (ptmm) cc_final: 0.8688 (ptmt) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2660 time to fit residues: 79.0803 Evaluate side-chains 150 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 18 optimal weight: 50.0000 chunk 26 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 575 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 HIS ** E 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.060318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.050962 restraints weight = 92341.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.052480 restraints weight = 54652.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.053571 restraints weight = 37179.036| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15832 Z= 0.166 Angle : 0.631 8.246 21535 Z= 0.310 Chirality : 0.046 0.563 2771 Planarity : 0.004 0.048 2623 Dihedral : 7.308 58.862 3928 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: -0.71 (0.21), residues: 1620 helix: 0.43 (0.28), residues: 362 sheet: -0.15 (0.23), residues: 500 loop : -1.09 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 427 HIS 0.005 0.001 HIS C 352 PHE 0.014 0.001 PHE E 522 TYR 0.021 0.002 TYR D 217 ARG 0.006 0.001 ARG F 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3080.36 seconds wall clock time: 58 minutes 4.93 seconds (3484.93 seconds total)