Starting phenix.real_space_refine on Sat Apr 13 03:53:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uov_26655/04_2024/7uov_26655.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uov_26655/04_2024/7uov_26655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uov_26655/04_2024/7uov_26655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uov_26655/04_2024/7uov_26655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uov_26655/04_2024/7uov_26655.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uov_26655/04_2024/7uov_26655.pdb" } resolution = 2.75 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7914 atoms to isotropic. 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 117 5.16 5 C 12394 2.51 5 N 3155 2.21 5 O 4091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a GLU 404": "OE1" <-> "OE2" Residue "T TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 81": "OE1" <-> "OE2" Residue "S GLU 10": "OE1" <-> "OE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 122": "OD1" <-> "OD2" Residue "B ASP 130": "OD1" <-> "OD2" Residue "b ASP 268": "OD1" <-> "OD2" Residue "b GLU 404": "OE1" <-> "OE2" Residue "P ASP 93": "OD1" <-> "OD2" Residue "P ASP 105": "OD1" <-> "OD2" Residue "O ASP 90": "OD1" <-> "OD2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "c ASP 268": "OD1" <-> "OD2" Residue "c GLU 404": "OE1" <-> "OE2" Residue "R ASP 93": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19757 Number of models: 1 Model: "" Number of chains: 51 Chain: "H" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 777 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 813 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1480 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 2 Chain: "a" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1224 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "T" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "S" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "D" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 777 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "E" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 813 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1480 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 2 Chain: "b" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1224 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "P" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "O" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "F" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 777 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "G" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 813 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1480 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 2 Chain: "c" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1224 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "R" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "Q" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, '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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "m" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "n" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, '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: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "x" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.64, per 1000 atoms: 0.54 Number of scatterers: 19757 At special positions: 0 Unit cell: (145.86, 147.84, 112.86, 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 117 16.00 O 4091 8.00 N 3155 7.00 C 12394 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN V 4 " - " MAN V 5 " " MAN Z 4 " - " MAN Z 5 " " MAN j 4 " - " MAN j 5 " " MAN p 4 " - " MAN p 5 " " MAN u 4 " - " MAN u 5 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " " BMA V 3 " - " MAN V 4 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " " BMA j 3 " - " MAN j 4 " " BMA m 3 " - " MAN m 4 " " BMA n 3 " - " MAN n 4 " " BMA p 3 " - " MAN p 4 " " BMA u 3 " - " MAN u 4 " " BMA x 3 " - " MAN x 4 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " " BMA V 3 " - " MAN V 6 " " BMA Y 3 " - " MAN Y 5 " " BMA Z 3 " - " MAN Z 6 " " BMA j 3 " - " MAN j 6 " " BMA m 3 " - " MAN m 5 " " BMA p 3 " - " MAN p 6 " " BMA u 3 " - " MAN u 6 " " BMA x 3 " - " MAN x 5 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " 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 m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " BETA1-6 " NAG K 1 " - " FUC K 5 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG M 1 " - " FUC M 4 " " NAG X 1 " - " FUC X 4 " " NAG Y 1 " - " FUC Y 6 " " NAG d 1 " - " FUC d 4 " " NAG e 1 " - " FUC e 4 " " NAG l 1 " - " FUC l 4 " " NAG m 1 " - " FUC m 6 " " NAG n 1 " - " FUC n 5 " " NAG r 1 " - " FUC r 4 " " NAG w 1 " - " FUC w 4 " " NAG x 1 " - " FUC x 6 " NAG-ASN " NAG A 301 " - " ASN A 99 " " NAG I 1 " - " ASN A 79 " " NAG J 1 " - " ASN A 89 " " NAG K 1 " - " ASN A 109 " " NAG M 1 " - " ASN A 119 " " NAG N 1 " - " ASN A 167 " " NAG U 1 " - " ASN A 224 " " NAG V 1 " - " ASN a 365 " " NAG W 1 " - " ASN a 373 " " NAG X 1 " - " ASN a 390 " " NAG Y 1 " - " ASN a 395 " " NAG Z 1 " - " ASN B 89 " " NAG d 1 " - " ASN B 109 " " NAG e 1 " - " ASN B 119 " " NAG f 1 " - " ASN B 167 " " NAG g 1 " - " ASN B 79 " " NAG h 1 " - " ASN B 99 " " NAG i 1 " - " ASN B 224 " " NAG j 1 " - " ASN b 365 " " NAG k 1 " - " ASN b 373 " " NAG l 1 " - " ASN b 390 " " NAG m 1 " - " ASN b 395 " " NAG n 1 " - " ASN C 109 " " NAG o 1 " - " ASN C 79 " " NAG p 1 " - " ASN C 89 " " NAG q 1 " - " ASN C 99 " " NAG r 1 " - " ASN C 119 " " NAG s 1 " - " ASN C 167 " " NAG t 1 " - " ASN C 224 " " NAG u 1 " - " ASN c 365 " " NAG v 1 " - " ASN c 373 " " NAG w 1 " - " ASN c 390 " " NAG x 1 " - " ASN c 395 " Time building additional restraints: 10.77 Conformation dependent library (CDL) restraints added in 3.3 seconds 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4266 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 44 sheets defined 21.1% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.007A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.505A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 79 " --> pdb=" O GLU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 157 through 161 removed outlier: 4.068A pdb=" N LYS A 161 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.507A pdb=" N LEU A 203 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'a' and resid 294 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 307 through 326 Processing helix chain 'a' and resid 333 through 341 Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.825A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 398 Processing helix chain 'a' and resid 399 through 416 removed outlier: 3.506A pdb=" N GLN a 416 " --> pdb=" O THR a 412 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 83 removed outlier: 3.736A pdb=" N PHE T 83 " --> pdb=" O SER T 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.990A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.799A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.788A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.566A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN B 79 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.768A pdb=" N LYS B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.590A pdb=" N GLY B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.865A pdb=" N ILE B 201 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 202 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 removed outlier: 4.070A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'b' and resid 294 through 300 removed outlier: 3.728A pdb=" N LYS b 300 " --> pdb=" O THR b 296 " (cutoff:3.500A) Processing helix chain 'b' and resid 301 through 303 No H-bonds generated for 'chain 'b' and resid 301 through 303' Processing helix chain 'b' and resid 307 through 326 Processing helix chain 'b' and resid 333 through 340 Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.885A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 416 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.902A pdb=" N PHE P 83 " --> pdb=" O SER P 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.696A pdb=" N THR O 91 " --> pdb=" O SER O 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 65 No H-bonds generated for 'chain 'F' and resid 63 through 65' Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.801A pdb=" N LYS C 161 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.942A pdb=" N ILE C 201 " --> pdb=" O GLY C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'c' and resid 294 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 326 Processing helix chain 'c' and resid 333 through 340 Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.834A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 416 removed outlier: 3.792A pdb=" N GLN c 416 " --> pdb=" O THR c 412 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'Q' and resid 28 through 32 Processing helix chain 'Q' and resid 87 through 91 removed outlier: 4.012A pdb=" N THR Q 91 " --> pdb=" O SER Q 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 20 through 23 removed outlier: 3.653A pdb=" N PHE H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.250A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG H 97 " --> pdb=" O ASP H 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.622A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.622A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA7, first strand: chain 'A' and resid 84 through 87 Processing sheet with id=AA8, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AA9, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AB1, first strand: chain 'T' and resid 10 through 11 removed outlier: 6.555A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 10 through 11 removed outlier: 3.720A pdb=" N SER T 97 " --> pdb=" O GLN T 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 19 through 29 removed outlier: 6.090A pdb=" N THR T 69 " --> pdb=" O ALA T 25 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 4 through 5 removed outlier: 3.612A pdb=" N VAL S 5 " --> pdb=" O LYS S 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 57 through 60 removed outlier: 6.560A pdb=" N TRP S 36 " --> pdb=" O MET S 48 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP S 50 " --> pdb=" O ILE S 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE S 34 " --> pdb=" O TRP S 50 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N CYS S 96 " --> pdb=" O TRP S 118 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TRP S 118 " --> pdb=" O CYS S 96 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG S 98 " --> pdb=" O ASP S 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 57 through 60 removed outlier: 6.560A pdb=" N TRP S 36 " --> pdb=" O MET S 48 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP S 50 " --> pdb=" O ILE S 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE S 34 " --> pdb=" O TRP S 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 19 through 23 Processing sheet with id=AB8, first strand: chain 'D' and resid 57 through 59 removed outlier: 5.509A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR D 99 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU D 111 " --> pdb=" O TYR D 99 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 4 through 6 removed outlier: 4.108A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.076A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AC4, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AC5, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AC6, first strand: chain 'P' and resid 4 through 5 Processing sheet with id=AC7, first strand: chain 'P' and resid 10 through 11 removed outlier: 6.730A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR P 53 " --> pdb=" O TYR P 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 10 through 11 removed outlier: 3.867A pdb=" N SER P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 4 through 5 Processing sheet with id=AD1, first strand: chain 'O' and resid 57 through 60 removed outlier: 6.801A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TRP O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE O 34 " --> pdb=" O TRP O 50 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL O 117 " --> pdb=" O ARG O 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 57 through 60 removed outlier: 6.801A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TRP O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE O 34 " --> pdb=" O TRP O 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 19 through 23 Processing sheet with id=AD4, first strand: chain 'F' and resid 57 through 58 removed outlier: 5.814A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU F 50 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TRP F 34 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG F 97 " --> pdb=" O ASP F 112 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR F 108 " --> pdb=" O TYR F 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.632A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AD8, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 87 Processing sheet with id=AE1, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AE2, first strand: chain 'c' and resid 388 through 389 Processing sheet with id=AE3, first strand: chain 'R' and resid 10 through 11 removed outlier: 6.471A pdb=" N GLN R 37 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU R 46 " --> pdb=" O GLN R 37 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 10 through 11 removed outlier: 3.723A pdb=" N SER R 97 " --> pdb=" O GLN R 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 19 through 24 Processing sheet with id=AE6, first strand: chain 'Q' and resid 4 through 5 Processing sheet with id=AE7, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.674A pdb=" N TRP Q 36 " --> pdb=" O MET Q 48 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N CYS Q 96 " --> pdb=" O TRP Q 118 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TRP Q 118 " --> pdb=" O CYS Q 96 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG Q 98 " --> pdb=" O ASP Q 116 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.674A pdb=" N TRP Q 36 " --> pdb=" O MET Q 48 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) 780 hydrogen bonds defined for protein. 1944 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.00 Time building geometry restraints manager: 11.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5923 1.34 - 1.46: 5348 1.46 - 1.58: 8750 1.58 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 20195 Sorted by residual: bond pdb=" C1 NAG w 1 " pdb=" O5 NAG w 1 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C3 BMA x 3 " pdb=" O3 BMA x 3 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C1 NAG e 1 " pdb=" O5 NAG e 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.36e+00 bond pdb=" C5 MAN n 4 " pdb=" O5 MAN n 4 " ideal model delta sigma weight residual 1.418 1.469 -0.051 2.00e-02 2.50e+03 6.39e+00 bond pdb=" C3 BMA m 3 " pdb=" O3 BMA m 3 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.25e+00 ... (remaining 20190 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.26: 475 106.26 - 113.26: 11639 113.26 - 120.27: 6631 120.27 - 127.27: 8427 127.27 - 134.28: 250 Bond angle restraints: 27422 Sorted by residual: angle pdb=" C PHE S 54 " pdb=" N ASN S 55 " pdb=" CA ASN S 55 " ideal model delta sigma weight residual 121.54 130.29 -8.75 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C PHE O 54 " pdb=" N ASN O 55 " pdb=" CA ASN O 55 " ideal model delta sigma weight residual 125.66 133.60 -7.94 1.85e+00 2.92e-01 1.84e+01 angle pdb=" C LEU c 394 " pdb=" N ASN c 395 " pdb=" CA ASN c 395 " ideal model delta sigma weight residual 122.74 116.60 6.14 1.82e+00 3.02e-01 1.14e+01 angle pdb=" C ILE T 30 " pdb=" N ASN T 31 " pdb=" CA ASN T 31 " ideal model delta sigma weight residual 121.54 127.47 -5.93 1.91e+00 2.74e-01 9.64e+00 angle pdb=" C ASN A 119 " pdb=" CA ASN A 119 " pdb=" CB ASN A 119 " ideal model delta sigma weight residual 110.81 115.92 -5.11 1.65e+00 3.67e-01 9.61e+00 ... (remaining 27417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.14: 12416 24.14 - 48.28: 673 48.28 - 72.42: 125 72.42 - 96.56: 160 96.56 - 120.70: 104 Dihedral angle restraints: 13478 sinusoidal: 6809 harmonic: 6669 Sorted by residual: dihedral pdb=" CB CYS a 364 " pdb=" SG CYS a 364 " pdb=" SG CYS a 385 " pdb=" CB CYS a 385 " ideal model delta sinusoidal sigma weight residual -86.00 -171.68 85.68 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS c 364 " pdb=" SG CYS c 364 " pdb=" SG CYS c 385 " pdb=" CB CYS c 385 " ideal model delta sinusoidal sigma weight residual -86.00 -168.53 82.53 1 1.00e+01 1.00e-02 8.35e+01 dihedral pdb=" CB CYS b 364 " pdb=" SG CYS b 364 " pdb=" SG CYS b 385 " pdb=" CB CYS b 385 " ideal model delta sinusoidal sigma weight residual -86.00 -164.39 78.39 1 1.00e+01 1.00e-02 7.67e+01 ... (remaining 13475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 3271 0.117 - 0.234: 103 0.234 - 0.351: 27 0.351 - 0.468: 1 0.468 - 0.585: 2 Chirality restraints: 3404 Sorted by residual: chirality pdb=" C1 NAG j 1 " pdb=" ND2 ASN b 365 " pdb=" C2 NAG j 1 " pdb=" O5 NAG j 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" C1 NAG g 1 " pdb=" ND2 ASN B 79 " pdb=" C2 NAG g 1 " pdb=" O5 NAG g 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.24e+00 chirality pdb=" C1 NAG x 1 " pdb=" ND2 ASN c 395 " pdb=" C2 NAG x 1 " pdb=" O5 NAG x 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 3401 not shown) Planarity restraints: 3293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 105 " -0.044 2.00e-02 2.50e+03 3.63e-02 3.29e+01 pdb=" CG TRP F 105 " 0.096 2.00e-02 2.50e+03 pdb=" CD1 TRP F 105 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP F 105 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP F 105 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 105 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 105 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 105 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 105 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP F 105 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 105 " -0.041 2.00e-02 2.50e+03 3.28e-02 2.69e+01 pdb=" CG TRP H 105 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 TRP H 105 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP H 105 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP H 105 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP H 105 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP H 105 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 105 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 105 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP H 105 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 109 " 0.037 2.00e-02 2.50e+03 3.49e-02 1.52e+01 pdb=" CG ASN C 109 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN C 109 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 109 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG n 1 " 0.036 2.00e-02 2.50e+03 ... (remaining 3290 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 756 2.72 - 3.26: 18875 3.26 - 3.81: 31371 3.81 - 4.35: 39525 4.35 - 4.90: 68063 Nonbonded interactions: 158590 Sorted by model distance: nonbonded pdb=" OD1 ASP G 82 " pdb=" OH TYR G 86 " model vdw 2.171 2.440 nonbonded pdb=" OD1 ASN c 395 " pdb=" N2 NAG x 1 " model vdw 2.187 2.520 nonbonded pdb=" OD1 ASN C 167 " pdb=" OG SER C 169 " model vdw 2.237 2.440 nonbonded pdb=" O GLY Q 66 " pdb=" NH1 ARG Q 84 " model vdw 2.240 2.520 nonbonded pdb=" NZ LYS A 116 " pdb=" O7 NAG N 1 " model vdw 2.254 2.520 ... (remaining 158585 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 59 through 259) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'f' selection = chain 'g' selection = chain 'o' selection = chain 's' } ncs_group { reference = (chain 'J' and resid 1 through 5) selection = (chain 'V' and resid 1 through 5) selection = (chain 'Y' and resid 1 through 5) selection = (chain 'Z' and resid 1 through 5) selection = (chain 'j' and resid 1 through 5) selection = (chain 'm' and resid 1 through 5) selection = (chain 'p' and resid 1 through 5) selection = (chain 'u' and resid 1 through 5) selection = (chain 'x' and resid 1 through 5) } ncs_group { reference = chain 'K' selection = chain 'n' } ncs_group { reference = chain 'M' selection = chain 'X' selection = chain 'd' selection = chain 'e' selection = chain 'l' selection = chain 'r' selection = chain 'w' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'U' selection = chain 'W' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'q' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.020 Extract box with map and model: 28.370 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 56.880 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.320 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:16.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.005 0.073 20195 Z= 0.295 Angle : 0.818 8.755 27422 Z= 0.353 Chirality : 0.054 0.585 3404 Planarity : 0.004 0.057 3260 Dihedral : 20.504 120.698 9122 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.15 (0.18), residues: 2250 helix: 0.82 (0.29), residues: 351 sheet: 0.84 (0.20), residues: 669 loop : -0.50 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.002 TRP F 105 HIS 0.008 0.001 HIS B 93 PHE 0.013 0.001 PHE b 399 TYR 0.012 0.001 TYR F 101 ARG 0.013 0.001 ARG G 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 429 time to evaluate : 2.177 Fit side-chains revert: symmetry clash REVERT: L 83 PHE cc_start: 0.6594 (m-80) cc_final: 0.6382 (m-80) REVERT: D 38 ARG cc_start: 0.7856 (ttp-170) cc_final: 0.7512 (ttp-170) REVERT: E 27 GLN cc_start: 0.8821 (pm20) cc_final: 0.8470 (pm20) REVERT: E 97 THR cc_start: 0.8576 (m) cc_final: 0.8363 (t) REVERT: P 79 GLN cc_start: 0.7734 (mt0) cc_final: 0.7483 (mm110) REVERT: Q 13 LYS cc_start: 0.8872 (pptt) cc_final: 0.8595 (ttpt) outliers start: 0 outliers final: 2 residues processed: 429 average time/residue: 1.6524 time to fit residues: 781.2106 Evaluate side-chains 356 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 354 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 411 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 0.0270 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 201 optimal weight: 10.0000 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN B 127 ASN B 146 ASN F 76 ASN C 230 HIS c 406 GLN c 409 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20195 Z= 0.190 Angle : 0.673 10.858 27422 Z= 0.313 Chirality : 0.045 0.461 3404 Planarity : 0.004 0.049 3260 Dihedral : 16.383 113.044 5028 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.41 % Allowed : 11.92 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.27 (0.18), residues: 2250 helix: 0.89 (0.28), residues: 387 sheet: 0.95 (0.20), residues: 681 loop : -0.49 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 105 HIS 0.007 0.001 HIS B 93 PHE 0.013 0.001 PHE F 78 TYR 0.019 0.001 TYR R 49 ARG 0.010 0.001 ARG P 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 378 time to evaluate : 2.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8081 (ptt180) REVERT: E 27 GLN cc_start: 0.8819 (pm20) cc_final: 0.8468 (pm20) REVERT: E 97 THR cc_start: 0.8601 (m) cc_final: 0.8333 (t) REVERT: G 17 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7679 (tm-30) REVERT: Q 13 LYS cc_start: 0.8877 (pptt) cc_final: 0.8598 (ttpt) outliers start: 28 outliers final: 13 residues processed: 391 average time/residue: 1.6367 time to fit residues: 706.4850 Evaluate side-chains 364 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 350 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain Q residue 22 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 0.0980 chunk 62 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 201 optimal weight: 0.0980 chunk 218 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 162 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 38 GLN S 39 GLN B 146 ASN b 295 ASN P 31 ASN O 120 GLN F 76 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 409 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20195 Z= 0.223 Angle : 0.670 11.044 27422 Z= 0.313 Chirality : 0.045 0.457 3404 Planarity : 0.004 0.055 3260 Dihedral : 13.752 116.890 5024 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.77 % Allowed : 15.64 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.39 (0.18), residues: 2250 helix: 1.35 (0.29), residues: 366 sheet: 0.95 (0.20), residues: 681 loop : -0.47 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP b 386 HIS 0.006 0.001 HIS B 93 PHE 0.013 0.001 PHE F 78 TYR 0.022 0.001 TYR R 49 ARG 0.013 0.001 ARG G 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 369 time to evaluate : 2.201 Fit side-chains revert: symmetry clash REVERT: L 89 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8428 (pt0) REVERT: S 12 LYS cc_start: 0.8421 (mtpp) cc_final: 0.8174 (mttp) REVERT: S 82 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7212 (tm-30) REVERT: E 27 GLN cc_start: 0.8845 (pm20) cc_final: 0.8474 (pm20) REVERT: E 45 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7349 (ptt90) REVERT: B 116 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8432 (mttt) REVERT: B 119 ASN cc_start: 0.6726 (m110) cc_final: 0.5172 (p0) REVERT: R 24 ARG cc_start: 0.7883 (ttm110) cc_final: 0.7368 (ttm110) REVERT: R 70 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7165 (mm-30) REVERT: Q 13 LYS cc_start: 0.8878 (pptt) cc_final: 0.8599 (ttpt) outliers start: 55 outliers final: 28 residues processed: 396 average time/residue: 1.6432 time to fit residues: 718.0026 Evaluate side-chains 378 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 347 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain Q residue 22 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 135 optimal weight: 0.0170 chunk 202 optimal weight: 7.9990 chunk 214 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 409 ASN ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** b 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 ASN O 120 GLN F 76 ASN c 409 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20195 Z= 0.237 Angle : 0.672 11.133 27422 Z= 0.316 Chirality : 0.044 0.464 3404 Planarity : 0.004 0.053 3260 Dihedral : 12.167 116.100 5024 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.27 % Allowed : 17.55 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.23 (0.18), residues: 2250 helix: 1.02 (0.28), residues: 384 sheet: 0.90 (0.20), residues: 687 loop : -0.58 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 386 HIS 0.005 0.001 HIS B 93 PHE 0.016 0.001 PHE G 83 TYR 0.024 0.001 TYR R 49 ARG 0.011 0.001 ARG G 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 363 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 82 ASP cc_start: 0.7856 (m-30) cc_final: 0.7575 (m-30) REVERT: a 404 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: S 12 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8195 (mttp) REVERT: S 82 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7191 (tm-30) REVERT: E 27 GLN cc_start: 0.8862 (pm20) cc_final: 0.8476 (pm20) REVERT: E 45 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7306 (ptt90) REVERT: P 83 PHE cc_start: 0.6708 (m-80) cc_final: 0.6224 (m-80) REVERT: G 17 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: Q 13 LYS cc_start: 0.8888 (pptt) cc_final: 0.8602 (ttpt) outliers start: 65 outliers final: 31 residues processed: 399 average time/residue: 1.6176 time to fit residues: 713.0859 Evaluate side-chains 375 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 341 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 404 GLU Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain Q residue 22 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 192 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 409 ASN T 89 GLN b 295 ASN P 31 ASN O 120 GLN F 76 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 406 GLN c 409 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20195 Z= 0.347 Angle : 0.720 11.382 27422 Z= 0.341 Chirality : 0.046 0.463 3404 Planarity : 0.004 0.057 3260 Dihedral : 11.823 116.702 5024 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.17 % Allowed : 18.90 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.07 (0.18), residues: 2250 helix: 0.89 (0.28), residues: 384 sheet: 0.81 (0.20), residues: 669 loop : -0.66 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 386 HIS 0.005 0.001 HIS B 93 PHE 0.016 0.001 PHE b 399 TYR 0.020 0.001 TYR R 49 ARG 0.012 0.001 ARG G 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 348 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7998 (ptt180) REVERT: S 82 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7179 (tm-30) REVERT: E 27 GLN cc_start: 0.8897 (pm20) cc_final: 0.8470 (pm20) REVERT: E 45 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7274 (ptt90) REVERT: P 83 PHE cc_start: 0.6789 (m-80) cc_final: 0.6295 (m-80) REVERT: P 105 ASP cc_start: 0.5273 (p0) cc_final: 0.4920 (p0) REVERT: Q 13 LYS cc_start: 0.8910 (pptt) cc_final: 0.8629 (ttpt) outliers start: 83 outliers final: 45 residues processed: 400 average time/residue: 1.6130 time to fit residues: 713.4231 Evaluate side-chains 382 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 335 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 404 GLU Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 365 ASN Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain Q residue 116 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 112 optimal weight: 0.0980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 409 ASN P 31 ASN O 120 GLN F 76 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 405 GLN c 409 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20195 Z= 0.206 Angle : 0.675 10.152 27422 Z= 0.319 Chirality : 0.044 0.461 3404 Planarity : 0.004 0.065 3260 Dihedral : 11.119 116.028 5024 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.67 % Allowed : 20.26 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.18), residues: 2250 helix: 1.01 (0.28), residues: 384 sheet: 0.84 (0.20), residues: 693 loop : -0.67 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 34 HIS 0.004 0.001 HIS B 93 PHE 0.016 0.001 PHE G 83 TYR 0.018 0.001 TYR R 49 ARG 0.015 0.001 ARG G 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 356 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8007 (ptt180) REVERT: H 66 ARG cc_start: 0.8341 (ptt90) cc_final: 0.7868 (ttp80) REVERT: S 82 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7141 (tm-30) REVERT: D 72 ASP cc_start: 0.7252 (t0) cc_final: 0.6803 (t0) REVERT: E 27 GLN cc_start: 0.8885 (pm20) cc_final: 0.8469 (pm20) REVERT: E 45 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7278 (ptt90) REVERT: P 83 PHE cc_start: 0.6703 (m-80) cc_final: 0.6276 (m-80) REVERT: P 105 ASP cc_start: 0.5302 (p0) cc_final: 0.5092 (p0) REVERT: G 17 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: Q 13 LYS cc_start: 0.8899 (pptt) cc_final: 0.8615 (ttpt) outliers start: 73 outliers final: 37 residues processed: 406 average time/residue: 1.6165 time to fit residues: 725.2801 Evaluate side-chains 374 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 334 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 404 GLU Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain Q residue 116 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 180 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 409 ASN T 42 GLN b 295 ASN O 120 GLN F 76 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 409 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20195 Z= 0.260 Angle : 0.686 10.089 27422 Z= 0.326 Chirality : 0.044 0.463 3404 Planarity : 0.004 0.068 3260 Dihedral : 10.789 115.631 5024 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.97 % Allowed : 20.81 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.18), residues: 2250 helix: 0.97 (0.28), residues: 384 sheet: 0.82 (0.20), residues: 693 loop : -0.68 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 47 HIS 0.004 0.001 HIS B 93 PHE 0.014 0.001 PHE b 399 TYR 0.026 0.001 TYR R 49 ARG 0.018 0.001 ARG G 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 349 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8002 (ptt180) REVERT: S 82 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7258 (tm-30) REVERT: E 27 GLN cc_start: 0.8896 (pm20) cc_final: 0.8473 (pm20) REVERT: E 45 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7249 (ptt90) REVERT: B 201 ILE cc_start: 0.7169 (OUTLIER) cc_final: 0.6933 (pt) REVERT: b 415 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7840 (mp) REVERT: b 416 GLN cc_start: 0.6318 (mp10) cc_final: 0.5777 (mp10) REVERT: P 83 PHE cc_start: 0.6709 (m-80) cc_final: 0.6289 (m-80) REVERT: G 17 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7480 (tm-30) REVERT: Q 13 LYS cc_start: 0.8901 (pptt) cc_final: 0.8616 (ttpt) outliers start: 79 outliers final: 51 residues processed: 399 average time/residue: 1.5560 time to fit residues: 687.9849 Evaluate side-chains 391 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 336 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 404 GLU Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 365 ASN Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 116 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 127 optimal weight: 0.1980 chunk 64 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 136 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 409 ASN T 42 GLN O 120 GLN F 76 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 405 GLN c 409 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20195 Z= 0.228 Angle : 0.690 10.016 27422 Z= 0.328 Chirality : 0.044 0.458 3404 Planarity : 0.004 0.076 3260 Dihedral : 10.304 115.280 5024 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.77 % Allowed : 21.77 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.18), residues: 2250 helix: 1.01 (0.28), residues: 384 sheet: 0.77 (0.20), residues: 687 loop : -0.64 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 47 HIS 0.004 0.001 HIS B 93 PHE 0.017 0.001 PHE G 83 TYR 0.027 0.001 TYR R 49 ARG 0.019 0.001 ARG G 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 345 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8000 (ptt180) REVERT: S 82 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7266 (tm-30) REVERT: E 27 GLN cc_start: 0.8890 (pm20) cc_final: 0.8476 (pm20) REVERT: E 45 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7253 (ptt90) REVERT: b 416 GLN cc_start: 0.6223 (mp10) cc_final: 0.5702 (mp10) REVERT: P 83 PHE cc_start: 0.6732 (m-80) cc_final: 0.6405 (m-80) REVERT: P 105 ASP cc_start: 0.5545 (p0) cc_final: 0.5203 (p0) REVERT: G 17 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7609 (tm-30) REVERT: Q 13 LYS cc_start: 0.8893 (pptt) cc_final: 0.8608 (ttpt) outliers start: 75 outliers final: 48 residues processed: 396 average time/residue: 1.5841 time to fit residues: 693.8006 Evaluate side-chains 387 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 337 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 404 GLU Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 116 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 0.5980 chunk 204 optimal weight: 0.0010 chunk 187 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 61 optimal weight: 0.0270 chunk 180 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 overall best weight: 0.5046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 409 ASN T 31 ASN T 42 GLN D 76 ASN b 295 ASN O 120 GLN F 76 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 406 GLN c 409 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20195 Z= 0.175 Angle : 0.671 9.853 27422 Z= 0.318 Chirality : 0.043 0.461 3404 Planarity : 0.004 0.081 3260 Dihedral : 9.680 114.422 5024 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.97 % Allowed : 22.37 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.18), residues: 2250 helix: 1.12 (0.28), residues: 384 sheet: 0.88 (0.20), residues: 666 loop : -0.61 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 34 HIS 0.004 0.001 HIS B 93 PHE 0.011 0.001 PHE F 78 TYR 0.029 0.001 TYR R 49 ARG 0.019 0.001 ARG G 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 355 time to evaluate : 2.084 Fit side-chains revert: symmetry clash REVERT: L 36 TYR cc_start: 0.7852 (m-80) cc_final: 0.7416 (m-80) REVERT: a 404 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: S 82 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7189 (tm-30) REVERT: E 27 GLN cc_start: 0.8866 (pm20) cc_final: 0.8467 (pm20) REVERT: E 42 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: P 81 GLU cc_start: 0.7745 (pm20) cc_final: 0.7228 (pm20) REVERT: P 83 PHE cc_start: 0.6700 (m-80) cc_final: 0.6360 (m-80) REVERT: P 105 ASP cc_start: 0.5358 (p0) cc_final: 0.5036 (p0) REVERT: O 13 LYS cc_start: 0.8411 (tppt) cc_final: 0.7954 (tptp) REVERT: F 63 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8756 (pp) REVERT: G 17 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7548 (tm-30) REVERT: Q 13 LYS cc_start: 0.8879 (pptt) cc_final: 0.8594 (ttpt) outliers start: 59 outliers final: 38 residues processed: 396 average time/residue: 1.6809 time to fit residues: 735.1639 Evaluate side-chains 386 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 345 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 404 GLU Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain Q residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 221 optimal weight: 0.7980 chunk 203 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 409 ASN ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 120 GLN F 76 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 405 GLN c 409 ASN Q 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20195 Z= 0.205 Angle : 0.685 12.310 27422 Z= 0.324 Chirality : 0.043 0.459 3404 Planarity : 0.004 0.086 3260 Dihedral : 9.535 114.305 5024 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.31 % Allowed : 23.38 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.18), residues: 2250 helix: 1.10 (0.28), residues: 384 sheet: 0.89 (0.21), residues: 666 loop : -0.60 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 34 HIS 0.004 0.001 HIS B 93 PHE 0.019 0.001 PHE G 83 TYR 0.030 0.001 TYR R 49 ARG 0.020 0.001 ARG P 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 353 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 36 TYR cc_start: 0.7848 (m-80) cc_final: 0.7434 (m-80) REVERT: S 82 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7265 (tm-30) REVERT: E 27 GLN cc_start: 0.8871 (pm20) cc_final: 0.8472 (pm20) REVERT: E 42 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.7025 (tm-30) REVERT: P 83 PHE cc_start: 0.6715 (m-80) cc_final: 0.6330 (m-80) REVERT: P 105 ASP cc_start: 0.5347 (p0) cc_final: 0.5029 (p0) REVERT: F 63 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8754 (pp) REVERT: G 17 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7561 (tm-30) REVERT: Q 13 LYS cc_start: 0.8867 (pptt) cc_final: 0.8587 (ttpt) outliers start: 46 outliers final: 36 residues processed: 382 average time/residue: 1.6279 time to fit residues: 686.2919 Evaluate side-chains 383 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 345 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 404 GLU Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain Q residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 5.9990 chunk 187 optimal weight: 0.4980 chunk 53 optimal weight: 6.9990 chunk 162 optimal weight: 0.7980 chunk 26 optimal weight: 0.0670 chunk 48 optimal weight: 0.7980 chunk 176 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 409 ASN ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 295 ASN O 120 GLN F 76 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 409 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.100264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.072060 restraints weight = 41351.653| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.52 r_work: 0.2945 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20195 Z= 0.184 Angle : 0.689 11.901 27422 Z= 0.326 Chirality : 0.042 0.459 3404 Planarity : 0.004 0.075 3260 Dihedral : 9.272 113.911 5024 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.11 % Allowed : 23.63 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.24 (0.18), residues: 2250 helix: 1.12 (0.28), residues: 384 sheet: 0.90 (0.21), residues: 666 loop : -0.58 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 34 HIS 0.004 0.001 HIS B 93 PHE 0.012 0.001 PHE F 78 TYR 0.029 0.001 TYR R 49 ARG 0.018 0.001 ARG G 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10125.07 seconds wall clock time: 182 minutes 19.46 seconds (10939.46 seconds total)