Starting phenix.real_space_refine on Sat Mar 16 21:19:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l89_23226/03_2024/7l89_23226_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l89_23226/03_2024/7l89_23226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l89_23226/03_2024/7l89_23226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l89_23226/03_2024/7l89_23226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l89_23226/03_2024/7l89_23226_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l89_23226/03_2024/7l89_23226_updated.pdb" } resolution = 3.8 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 9758 2.51 5 N 2618 2.21 5 O 3204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 621": "OE1" <-> "OE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15679 Number of models: 1 Model: "" Number of chains: 51 Chain: "H" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 570 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'TRANS': 113} Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'UNK:plan-1': 114} Unresolved non-hydrogen planarities: 114 Chain: "L" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 485 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'TRANS': 96} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 291 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'UNK:plan-1': 97} Unresolved non-hydrogen planarities: 97 Chain: "E" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "A" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" 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: "B" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: 15 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 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: "E" 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 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: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" 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: "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 Time building chain proxies: 9.05, per 1000 atoms: 0.58 Number of scatterers: 15679 At special positions: 0 Unit cell: (128.75, 122.57, 152.44, 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 3204 8.00 N 2618 7.00 C 9758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.07 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS C 605 " distance=2.02 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.07 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.07 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.02 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA Y 3 " - " MAN Y 4 " " BMA l 3 " - " MAN l 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA Y 3 " - " MAN Y 5 " " BMA l 3 " - " MAN l 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 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 i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 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 q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 137 " " NAG B 601 " - " ASN B 133 " " NAG B 602 " - " ASN B 234 " " NAG B 603 " - " ASN B 88 " " NAG B 604 " - " ASN B 137 " " NAG C 701 " - " ASN C 637 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 339 " " NAG E 604 " - " ASN E 137 " " NAG F 701 " - " ASN F 637 " " NAG G 1 " - " ASN E 156 " " NAG I 1 " - " ASN E 197 " " NAG J 1 " - " ASN E 234 " " NAG K 1 " - " ASN E 262 " " NAG M 1 " - " ASN E 276 " " NAG N 1 " - " ASN E 295 " " NAG O 1 " - " ASN E 301 " " NAG P 1 " - " ASN E 332 " " NAG Q 1 " - " ASN E 386 " " NAG R 1 " - " ASN E 392 " " NAG S 1 " - " ASN E 448 " " NAG T 1 " - " ASN E 88 " " NAG U 1 " - " ASN F 611 " " NAG V 1 " - " ASN A 156 " " NAG W 1 " - " ASN A 197 " " NAG X 1 " - " ASN A 234 " " NAG Y 1 " - " ASN A 262 " " NAG Z 1 " - " ASN A 276 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN A 332 " " NAG c 1 " - " ASN A 386 " " NAG d 1 " - " ASN A 392 " " NAG e 1 " - " ASN A 448 " " NAG f 1 " - " ASN A 88 " " NAG g 1 " - " ASN C 611 " " NAG h 1 " - " ASN C 618 " " NAG i 1 " - " ASN B 156 " " NAG j 1 " - " ASN B 160 " " NAG k 1 " - " ASN B 197 " " NAG l 1 " - " ASN B 262 " " NAG m 1 " - " ASN B 276 " " NAG n 1 " - " ASN B 295 " " NAG o 1 " - " ASN B 301 " " NAG p 1 " - " ASN B 332 " " NAG q 1 " - " ASN B 386 " " NAG r 1 " - " ASN B 392 " " NAG s 1 " - " ASN B 448 " Time building additional restraints: 7.06 Conformation dependent library (CDL) restraints added in 2.7 seconds 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3566 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 29 sheets defined 24.5% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.693A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 335 through 353 removed outlier: 4.058A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 475 through 485 removed outlier: 3.776A pdb=" N ARG E 480 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU E 483 " --> pdb=" O ARG E 480 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TYR E 484 " --> pdb=" O SER E 481 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS E 485 " --> pdb=" O GLU E 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 543 removed outlier: 5.158A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU F 537 " --> pdb=" O ALA F 533 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL F 539 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 595 removed outlier: 3.709A pdb=" N GLN F 575 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU F 581 " --> pdb=" O ALA F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 628 through 634 Processing helix chain 'F' and resid 639 through 663 removed outlier: 3.703A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA F 662 " --> pdb=" O GLN F 658 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 335 through 347 Processing helix chain 'A' and resid 350 through 353 No H-bonds generated for 'chain 'A' and resid 350 through 353' Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.937A pdb=" N ARG A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 543 removed outlier: 4.800A pdb=" N MET C 535 " --> pdb=" O GLY C 531 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR C 536 " --> pdb=" O ALA C 532 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU C 537 " --> pdb=" O ALA C 533 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR C 538 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL C 539 " --> pdb=" O MET C 535 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 596 removed outlier: 3.784A pdb=" N LEU C 576 " --> pdb=" O GLY C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 622 No H-bonds generated for 'chain 'C' and resid 619 through 622' Processing helix chain 'C' and resid 628 through 634 Processing helix chain 'C' and resid 636 through 662 removed outlier: 3.882A pdb=" N THR C 639 " --> pdb=" O SER C 636 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLN C 640 " --> pdb=" O ASN C 637 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR C 643 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 661 " --> pdb=" O GLN C 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 99 through 116 removed outlier: 3.683A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 194 through 197 removed outlier: 4.488A pdb=" N ASN B 197 " --> pdb=" O ILE B 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 through 197' Processing helix chain 'B' and resid 335 through 353 removed outlier: 3.953A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 372 No H-bonds generated for 'chain 'B' and resid 369 through 372' Processing helix chain 'B' and resid 475 through 485 removed outlier: 3.805A pdb=" N ARG B 480 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 483 " --> pdb=" O ARG B 480 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TYR B 484 " --> pdb=" O SER B 481 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS B 485 " --> pdb=" O GLU B 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 543 removed outlier: 4.404A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 removed outlier: 3.764A pdb=" N LYS D 574 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 581 " --> pdb=" O ALA D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 622 No H-bonds generated for 'chain 'D' and resid 619 through 622' Processing helix chain 'D' and resid 628 through 634 Processing helix chain 'D' and resid 636 through 662 removed outlier: 3.953A pdb=" N THR D 639 " --> pdb=" O SER D 636 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR D 643 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 661 " --> pdb=" O GLN D 658 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'H' and resid 112 through 114 removed outlier: 4.181A pdb=" N UNK H 112 " --> pdb=" O UNK H 89 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N UNK H 34 " --> pdb=" O UNK H 94 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.390A pdb=" N UNK L 36 " --> pdb=" O UNK L 48 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N UNK L 97 " --> pdb=" O UNK L 93 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= D, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.801A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 130 through 133 Processing sheet with id= F, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= G, first strand: chain 'E' and resid 200 through 203 Processing sheet with id= H, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.475A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N ALA E 362 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.455A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 66 through 69 removed outlier: 3.536A pdb=" N UNK H 66 " --> pdb=" O UNK H 79 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N UNK H 79 " --> pdb=" O UNK H 66 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 301 through 308 removed outlier: 4.187A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.882A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= M, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.699A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= O, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= P, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= Q, first strand: chain 'A' and resid 200 through 203 Processing sheet with id= R, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.431A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N ALA A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.395A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 301 through 308 removed outlier: 3.920A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 5.998A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 35 through 40 Processing sheet with id= V, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.757A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 53 through 55 Processing sheet with id= X, first strand: chain 'B' and resid 130 through 133 Processing sheet with id= Y, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= Z, first strand: chain 'B' and resid 200 through 203 Processing sheet with id= AA, first strand: chain 'B' and resid 271 through 273 removed outlier: 6.252A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N PHE B 468 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ALA B 362 " --> pdb=" O PRO B 470 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 374 through 378 removed outlier: 4.324A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 301 through 308 removed outlier: 4.177A pdb=" N ASN B 301 " --> pdb=" O ILE B 323A" (cutoff:3.500A) removed outlier: 6.020A pdb=" N LYS B 305 " --> pdb=" O THR B 320 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N THR B 320 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE B 307 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N TYR B 318 " --> pdb=" O ILE B 307 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1095 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: 6.23 Time building geometry restraints manager: 7.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 2619 1.31 - 1.45: 4815 1.45 - 1.59: 8327 1.59 - 1.73: 59 1.73 - 1.87: 127 Bond restraints: 15947 Sorted by residual: bond pdb=" CB ASN A 195 " pdb=" CG ASN A 195 " ideal model delta sigma weight residual 1.516 1.347 0.169 2.50e-02 1.60e+03 4.57e+01 bond pdb=" CB ASN E 195 " pdb=" CG ASN E 195 " ideal model delta sigma weight residual 1.516 1.353 0.163 2.50e-02 1.60e+03 4.24e+01 bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.394 -0.068 1.10e-02 8.26e+03 3.87e+01 bond pdb=" C LYS D 655 " pdb=" O LYS D 655 " ideal model delta sigma weight residual 1.237 1.164 0.073 1.19e-02 7.06e+03 3.71e+01 bond pdb=" NE ARG B 503 " pdb=" CZ ARG B 503 " ideal model delta sigma weight residual 1.326 1.391 -0.065 1.10e-02 8.26e+03 3.44e+01 ... (remaining 15942 not shown) Histogram of bond angle deviations from ideal: 93.75 - 101.86: 50 101.86 - 109.98: 4571 109.98 - 118.10: 8325 118.10 - 126.21: 8435 126.21 - 134.33: 311 Bond angle restraints: 21692 Sorted by residual: angle pdb=" N ASP A 141 " pdb=" CA ASP A 141 " pdb=" C ASP A 141 " ideal model delta sigma weight residual 113.88 93.75 20.13 1.23e+00 6.61e-01 2.68e+02 angle pdb=" N LEU D 544 " pdb=" CA LEU D 544 " pdb=" C LEU D 544 " ideal model delta sigma weight residual 110.48 98.59 11.89 1.48e+00 4.57e-01 6.46e+01 angle pdb=" C CYS B 239 " pdb=" N PRO B 240 " pdb=" CA PRO B 240 " ideal model delta sigma weight residual 119.56 127.60 -8.04 1.02e+00 9.61e-01 6.22e+01 angle pdb=" C CYS A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta sigma weight residual 119.56 127.22 -7.66 1.02e+00 9.61e-01 5.64e+01 angle pdb=" N SER B 56 " pdb=" CA SER B 56 " pdb=" C SER B 56 " ideal model delta sigma weight residual 113.89 125.65 -11.76 1.58e+00 4.01e-01 5.54e+01 ... (remaining 21687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 10579 21.24 - 42.47: 210 42.47 - 63.71: 64 63.71 - 84.94: 26 84.94 - 106.18: 12 Dihedral angle restraints: 10891 sinusoidal: 5415 harmonic: 5476 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual 93.00 156.56 -63.56 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.28 -60.28 1 1.00e+01 1.00e-02 4.84e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 147.90 -54.90 1 1.00e+01 1.00e-02 4.08e+01 ... (remaining 10888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 2121 0.158 - 0.315: 494 0.315 - 0.473: 166 0.473 - 0.631: 8 0.631 - 0.789: 1 Chirality restraints: 2790 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-02 2.50e+03 1.55e+03 chirality pdb=" C1 NAG g 2 " pdb=" O4 NAG g 1 " pdb=" C2 NAG g 2 " pdb=" O5 NAG g 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-02 2.50e+03 3.69e+02 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 -2.67 0.27 2.00e-02 2.50e+03 1.84e+02 ... (remaining 2787 not shown) Planarity restraints: 2700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " 0.342 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG j 1 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " 0.155 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " -0.522 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 2 " -0.338 2.00e-02 2.50e+03 2.89e-01 1.05e+03 pdb=" C7 NAG h 2 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG h 2 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG h 2 " 0.510 2.00e-02 2.50e+03 pdb=" O7 NAG h 2 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 1 " 0.314 2.00e-02 2.50e+03 2.73e-01 9.34e+02 pdb=" C7 NAG h 1 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG h 1 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG h 1 " -0.479 2.00e-02 2.50e+03 pdb=" O7 NAG h 1 " 0.200 2.00e-02 2.50e+03 ... (remaining 2697 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 156 2.62 - 3.19: 13652 3.19 - 3.76: 21924 3.76 - 4.33: 33364 4.33 - 4.90: 51316 Nonbonded interactions: 120412 Sorted by model distance: nonbonded pdb=" O3 NAG A 605 " pdb=" O7 NAG A 605 " model vdw 2.051 2.440 nonbonded pdb=" O3 NAG g 2 " pdb=" O7 NAG g 2 " model vdw 2.119 2.440 nonbonded pdb=" O3 NAG g 1 " pdb=" O7 NAG g 1 " model vdw 2.266 2.440 nonbonded pdb=" N ASP A 141 " pdb=" N MET A 150 " model vdw 2.279 2.560 nonbonded pdb=" O UNK H 51 " pdb=" O UNK H 54 " model vdw 2.319 3.040 ... (remaining 120407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 503 or resid 601 through 604)) selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 519 through 664 or resid 701)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' 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 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' } ncs_group { reference = (chain 'H' and resid 20 through 116) selection = chain 'L' } ncs_group { reference = chain 'K' selection = chain 'Y' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.140 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 46.930 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.169 15947 Z= 1.472 Angle : 1.761 20.134 21692 Z= 1.101 Chirality : 0.153 0.789 2790 Planarity : 0.016 0.294 2646 Dihedral : 10.667 106.178 7226 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: 0.80 (0.20), residues: 1635 helix: -0.04 (0.24), residues: 378 sheet: 1.03 (0.22), residues: 474 loop : 0.70 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.009 TRP E 35 HIS 0.008 0.002 HIS E 374 PHE 0.024 0.007 PHE B 383 TYR 0.045 0.007 TYR B 486 ARG 0.010 0.001 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 579 ARG cc_start: 0.8872 (mtp180) cc_final: 0.8569 (mtm-85) REVERT: A 432 GLN cc_start: 0.8460 (mp10) cc_final: 0.8169 (mp10) REVERT: B 104 MET cc_start: 0.8639 (ttm) cc_final: 0.8404 (ttt) REVERT: B 342 LEU cc_start: 0.9451 (tp) cc_final: 0.9209 (tp) REVERT: D 573 ILE cc_start: 0.9047 (tp) cc_final: 0.8773 (tt) REVERT: D 659 ASP cc_start: 0.8383 (m-30) cc_final: 0.8171 (m-30) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3706 time to fit residues: 126.4784 Evaluate side-chains 133 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN E 328 GLN A 33 ASN A 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15947 Z= 0.236 Angle : 0.687 12.444 21692 Z= 0.349 Chirality : 0.047 0.387 2790 Planarity : 0.005 0.040 2646 Dihedral : 8.398 83.050 4061 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.80 % Allowed : 5.09 % Favored : 94.11 % 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: 0.81 (0.20), residues: 1635 helix: 0.49 (0.27), residues: 369 sheet: 1.00 (0.24), residues: 408 loop : 0.48 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 571 HIS 0.005 0.001 HIS B 66 PHE 0.018 0.002 PHE C 522 TYR 0.021 0.001 TYR A 217 ARG 0.005 0.001 ARG E 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 169 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 590 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8508 (mp10) REVERT: A 125 LEU cc_start: 0.9133 (tp) cc_final: 0.8884 (tt) REVERT: C 530 MET cc_start: 0.7616 (mtp) cc_final: 0.7303 (mtp) REVERT: C 535 MET cc_start: 0.8358 (mpp) cc_final: 0.8113 (mpp) outliers start: 12 outliers final: 3 residues processed: 177 average time/residue: 0.2933 time to fit residues: 75.7123 Evaluate side-chains 138 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 590 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 166 optimal weight: 0.0170 chunk 57 optimal weight: 0.9980 chunk 135 optimal weight: 0.0980 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN B 99 ASN D 618 ASN D 658 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15947 Z= 0.204 Angle : 0.571 10.453 21692 Z= 0.287 Chirality : 0.044 0.377 2790 Planarity : 0.004 0.044 2646 Dihedral : 7.495 71.825 4061 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.07 % Allowed : 6.49 % Favored : 92.44 % 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: 0.58 (0.21), residues: 1635 helix: 0.14 (0.27), residues: 369 sheet: 0.89 (0.24), residues: 450 loop : 0.37 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 571 HIS 0.004 0.001 HIS E 105 PHE 0.011 0.001 PHE B 53 TYR 0.018 0.001 TYR D 586 ARG 0.005 0.000 ARG E 476 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.9111 (tp) cc_final: 0.8591 (tt) REVERT: C 535 MET cc_start: 0.8466 (mpp) cc_final: 0.8186 (mpp) outliers start: 16 outliers final: 9 residues processed: 150 average time/residue: 0.2846 time to fit residues: 63.7968 Evaluate side-chains 132 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.1980 chunk 126 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 30.0000 chunk 80 optimal weight: 0.4980 chunk 113 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15947 Z= 0.401 Angle : 0.669 10.784 21692 Z= 0.327 Chirality : 0.046 0.307 2790 Planarity : 0.005 0.052 2646 Dihedral : 7.358 64.242 4061 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.94 % Allowed : 7.56 % Favored : 91.50 % 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: 0.53 (0.21), residues: 1635 helix: 0.33 (0.28), residues: 360 sheet: 0.90 (0.24), residues: 429 loop : 0.20 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 479 HIS 0.005 0.001 HIS A 330 PHE 0.018 0.002 PHE A 361 TYR 0.014 0.002 TYR C 586 ARG 0.006 0.001 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 535 MET cc_start: 0.8620 (mpp) cc_final: 0.8341 (mpp) REVERT: A 125 LEU cc_start: 0.9131 (tp) cc_final: 0.8550 (tt) REVERT: C 535 MET cc_start: 0.8448 (mpp) cc_final: 0.8142 (mpp) REVERT: B 161 MET cc_start: 0.8768 (tpt) cc_final: 0.8466 (tpt) REVERT: D 586 TYR cc_start: 0.9090 (t80) cc_final: 0.8734 (t80) outliers start: 14 outliers final: 12 residues processed: 131 average time/residue: 0.2913 time to fit residues: 57.3772 Evaluate side-chains 129 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain D residue 606 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 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 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15947 Z= 0.265 Angle : 0.563 9.727 21692 Z= 0.280 Chirality : 0.044 0.297 2790 Planarity : 0.004 0.047 2646 Dihedral : 6.877 59.116 4061 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.07 % Allowed : 7.76 % Favored : 91.16 % 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: 1635 helix: 0.31 (0.28), residues: 363 sheet: 0.83 (0.24), residues: 435 loop : 0.12 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 571 HIS 0.004 0.001 HIS E 105 PHE 0.010 0.001 PHE A 361 TYR 0.011 0.001 TYR C 586 ARG 0.011 0.000 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.524 Fit side-chains revert: symmetry clash REVERT: F 535 MET cc_start: 0.8609 (mpp) cc_final: 0.8394 (mpp) REVERT: C 535 MET cc_start: 0.8367 (mpp) cc_final: 0.8085 (mpp) outliers start: 16 outliers final: 13 residues processed: 133 average time/residue: 0.2768 time to fit residues: 55.2911 Evaluate side-chains 128 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 475 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 178 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15947 Z= 0.213 Angle : 0.541 10.341 21692 Z= 0.267 Chirality : 0.043 0.296 2790 Planarity : 0.004 0.048 2646 Dihedral : 6.518 56.991 4061 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.14 % Allowed : 8.17 % Favored : 90.70 % 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: 0.41 (0.21), residues: 1635 helix: 0.31 (0.28), residues: 363 sheet: 0.85 (0.24), residues: 435 loop : 0.07 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 479 HIS 0.004 0.001 HIS A 105 PHE 0.010 0.001 PHE C 522 TYR 0.010 0.001 TYR C 586 ARG 0.008 0.000 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.889 Fit side-chains revert: symmetry clash REVERT: C 535 MET cc_start: 0.8359 (mpp) cc_final: 0.8060 (mpp) outliers start: 17 outliers final: 11 residues processed: 134 average time/residue: 0.2890 time to fit residues: 58.1660 Evaluate side-chains 132 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 475 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 178 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15947 Z= 0.162 Angle : 0.513 9.515 21692 Z= 0.254 Chirality : 0.043 0.293 2790 Planarity : 0.004 0.047 2646 Dihedral : 6.177 58.929 4061 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.94 % Allowed : 8.10 % Favored : 90.96 % 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: 0.53 (0.21), residues: 1635 helix: 0.50 (0.29), residues: 351 sheet: 0.85 (0.26), residues: 399 loop : 0.18 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 479 HIS 0.003 0.001 HIS A 72 PHE 0.011 0.001 PHE A 53 TYR 0.010 0.001 TYR C 586 ARG 0.006 0.000 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 1.658 Fit side-chains revert: symmetry clash REVERT: F 579 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.8471 (ttp-170) REVERT: A 125 LEU cc_start: 0.9029 (tp) cc_final: 0.8515 (tt) REVERT: C 535 MET cc_start: 0.8349 (mpp) cc_final: 0.8053 (mpp) REVERT: C 641 ILE cc_start: 0.9240 (mp) cc_final: 0.9035 (mt) outliers start: 14 outliers final: 12 residues processed: 141 average time/residue: 0.3024 time to fit residues: 62.8412 Evaluate side-chains 143 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 475 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 140 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS D 618 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15947 Z= 0.304 Angle : 0.573 9.984 21692 Z= 0.281 Chirality : 0.044 0.287 2790 Planarity : 0.004 0.049 2646 Dihedral : 6.345 58.907 4061 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.07 % Allowed : 8.37 % Favored : 90.56 % 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: 0.46 (0.21), residues: 1635 helix: 0.50 (0.29), residues: 345 sheet: 0.94 (0.25), residues: 393 loop : 0.03 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 571 HIS 0.004 0.001 HIS A 105 PHE 0.013 0.002 PHE A 361 TYR 0.011 0.001 TYR E 486 ARG 0.010 0.001 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.854 Fit side-chains revert: symmetry clash REVERT: F 575 GLN cc_start: 0.8309 (tp40) cc_final: 0.7921 (tm-30) REVERT: F 653 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8109 (tm-30) REVERT: F 658 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8566 (tm-30) REVERT: C 535 MET cc_start: 0.8362 (mpp) cc_final: 0.8063 (mpp) REVERT: C 586 TYR cc_start: 0.8964 (t80) cc_final: 0.8741 (t80) outliers start: 16 outliers final: 13 residues processed: 134 average time/residue: 0.2737 time to fit residues: 56.0008 Evaluate side-chains 137 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain D residue 618 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 166 optimal weight: 0.0870 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 overall best weight: 0.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15947 Z= 0.183 Angle : 0.527 9.728 21692 Z= 0.260 Chirality : 0.043 0.289 2790 Planarity : 0.004 0.046 2646 Dihedral : 6.138 57.963 4061 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.00 % Allowed : 8.50 % Favored : 90.50 % 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: 0.54 (0.21), residues: 1635 helix: 0.56 (0.29), residues: 351 sheet: 0.84 (0.24), residues: 429 loop : 0.13 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 631 HIS 0.003 0.001 HIS A 105 PHE 0.010 0.001 PHE A 53 TYR 0.009 0.001 TYR C 586 ARG 0.011 0.000 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.760 Fit side-chains revert: symmetry clash REVERT: F 575 GLN cc_start: 0.8284 (tp40) cc_final: 0.7855 (tm-30) REVERT: F 653 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8118 (tm-30) REVERT: C 535 MET cc_start: 0.8320 (mpp) cc_final: 0.8008 (mpp) REVERT: C 586 TYR cc_start: 0.8951 (t80) cc_final: 0.8725 (t80) REVERT: D 633 LYS cc_start: 0.8904 (mmtm) cc_final: 0.8552 (mmtp) outliers start: 15 outliers final: 13 residues processed: 140 average time/residue: 0.2819 time to fit residues: 60.0104 Evaluate side-chains 135 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain D residue 618 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 15 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN A 99 ASN ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15947 Z= 0.319 Angle : 0.586 9.380 21692 Z= 0.287 Chirality : 0.044 0.278 2790 Planarity : 0.004 0.050 2646 Dihedral : 6.318 59.633 4061 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.07 % Allowed : 8.70 % Favored : 90.23 % 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: 0.46 (0.21), residues: 1635 helix: 0.54 (0.29), residues: 354 sheet: 0.98 (0.25), residues: 387 loop : -0.01 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 571 HIS 0.004 0.001 HIS A 105 PHE 0.014 0.002 PHE A 361 TYR 0.011 0.001 TYR C 586 ARG 0.011 0.000 ARG C 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 1.611 Fit side-chains revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7864 (p0) cc_final: 0.7613 (p0) REVERT: D 633 LYS cc_start: 0.8923 (mmtm) cc_final: 0.8595 (mmtp) outliers start: 16 outliers final: 15 residues processed: 132 average time/residue: 0.2948 time to fit residues: 59.7970 Evaluate side-chains 136 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain D residue 618 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 18 optimal weight: 30.0000 chunk 27 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.069103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.054040 restraints weight = 48274.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.055966 restraints weight = 25052.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.057293 restraints weight = 16850.890| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15947 Z= 0.179 Angle : 0.519 9.506 21692 Z= 0.257 Chirality : 0.043 0.285 2790 Planarity : 0.004 0.055 2646 Dihedral : 5.978 59.373 4061 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.80 % Allowed : 8.90 % Favored : 90.29 % 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: 0.51 (0.21), residues: 1635 helix: 0.62 (0.29), residues: 351 sheet: 0.86 (0.24), residues: 429 loop : 0.05 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 571 HIS 0.003 0.001 HIS A 105 PHE 0.011 0.001 PHE A 53 TYR 0.009 0.001 TYR C 586 ARG 0.013 0.000 ARG C 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2621.95 seconds wall clock time: 49 minutes 0.76 seconds (2940.76 seconds total)