Starting phenix.real_space_refine on Sat Mar 16 08:31:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd8_4521/03_2024/6qd8_4521_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd8_4521/03_2024/6qd8_4521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd8_4521/03_2024/6qd8_4521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd8_4521/03_2024/6qd8_4521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd8_4521/03_2024/6qd8_4521_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd8_4521/03_2024/6qd8_4521_updated.pdb" } resolution = 3.3 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= 0.004 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 8976 2.51 5 N 2394 2.21 5 O 2739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Z TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A ASP 49": "OD1" <-> "OD2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ASP 55": "OD1" <-> "OD2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 282": "OD1" <-> "OD2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "Y TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 552": "OD1" <-> "OD2" Residue "B ARG 559": "NH1" <-> "NH2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B ASP 607": "OD1" <-> "OD2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B ASP 621": "OD1" <-> "OD2" Residue "B PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C ASP 49": "OD1" <-> "OD2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ASP 55": "OD1" <-> "OD2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C ASP 127": "OD1" <-> "OD2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "C TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 247": "NH1" <-> "NH2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 258": "OE1" <-> "OE2" Residue "C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 282": "OD1" <-> "OD2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E ASP 49": "OD1" <-> "OD2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ASP 55": "OD1" <-> "OD2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E GLU 100": "OE1" <-> "OE2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "E GLU 112": "OE1" <-> "OE2" Residue "E GLU 120": "OE1" <-> "OE2" Residue "E ASP 127": "OD1" <-> "OD2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ASP 163": "OD1" <-> "OD2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 219": "NH1" <-> "NH2" Residue "E GLU 229": "OE1" <-> "OE2" Residue "E TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 235": "OE1" <-> "OE2" Residue "E TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 247": "NH1" <-> "NH2" Residue "E PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 258": "OE1" <-> "OE2" Residue "E TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 282": "OD1" <-> "OD2" Residue "E GLU 304": "OE1" <-> "OE2" Residue "F TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 552": "OD1" <-> "OD2" Residue "F ARG 559": "NH1" <-> "NH2" Residue "F GLU 578": "OE1" <-> "OE2" Residue "F ASP 607": "OD1" <-> "OD2" Residue "F ASP 614": "OD1" <-> "OD2" Residue "F ASP 621": "OD1" <-> "OD2" Residue "F PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 552": "OD1" <-> "OD2" Residue "D ARG 559": "NH1" <-> "NH2" Residue "D GLU 578": "OE1" <-> "OE2" Residue "D ASP 607": "OD1" <-> "OD2" Residue "D ASP 614": "OD1" <-> "OD2" Residue "D ASP 621": "OD1" <-> "OD2" Residue "D PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14154 Number of models: 1 Model: "" Number of chains: 18 Chain: "Z" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 795 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 97} Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 242} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "Y" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 795 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 97} Chain: "B" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1032 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 795 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 97} Chain: "H" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 866 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "C" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 242} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 242} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1032 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "D" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1032 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "W" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 866 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "Q" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 866 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} 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: "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: 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" 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: 7.58, per 1000 atoms: 0.54 Number of scatterers: 14154 At special positions: 0 Unit cell: (127.5, 136.85, 126.65, 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 45 16.00 O 2739 8.00 N 2394 7.00 C 8976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 609 " distance=1.96 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS D 609 " distance=2.09 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS F 609 " distance=2.06 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.04 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.02 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.04 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.02 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.04 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 96 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.05 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " 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-ASN " NAG B 701 " - " ASN B 618 " " NAG D 701 " - " ASN D 618 " " NAG F 701 " - " ASN F 618 " " NAG G 1 " - " ASN B 563 " " NAG I 1 " - " ASN F 563 " " NAG J 1 " - " ASN D 563 " Time building additional restraints: 5.26 Conformation dependent library (CDL) restraints added in 2.5 seconds 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 33 sheets defined 13.3% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 79 through 85 removed outlier: 3.866A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'B' and resid 539 through 541 No H-bonds generated for 'chain 'B' and resid 539 through 541' Processing helix chain 'B' and resid 551 through 575 removed outlier: 5.846A pdb=" N ILE B 555 " --> pdb=" O ASP B 552 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 560 " --> pdb=" O GLY B 557 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA B 562 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN B 567 " --> pdb=" O GLU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 597 Processing helix chain 'B' and resid 613 through 621 Processing helix chain 'C' and resid 60 through 62 No H-bonds generated for 'chain 'C' and resid 60 through 62' Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 79 through 85 removed outlier: 3.866A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'E' and resid 60 through 62 No H-bonds generated for 'chain 'E' and resid 60 through 62' Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 79 through 85 removed outlier: 3.866A pdb=" N LYS E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'F' and resid 539 through 541 No H-bonds generated for 'chain 'F' and resid 539 through 541' Processing helix chain 'F' and resid 551 through 575 removed outlier: 5.845A pdb=" N ILE F 555 " --> pdb=" O ASP F 552 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN F 560 " --> pdb=" O GLY F 557 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA F 562 " --> pdb=" O ARG F 559 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN F 567 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 597 Processing helix chain 'F' and resid 613 through 621 Processing helix chain 'D' and resid 539 through 541 No H-bonds generated for 'chain 'D' and resid 539 through 541' Processing helix chain 'D' and resid 551 through 575 removed outlier: 5.846A pdb=" N ILE D 555 " --> pdb=" O ASP D 552 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN D 560 " --> pdb=" O GLY D 557 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA D 562 " --> pdb=" O ARG D 559 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN D 567 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 597 Processing helix chain 'D' and resid 613 through 621 Processing sheet with id= A, first strand: chain 'Z' and resid 4 through 7 Processing sheet with id= B, first strand: chain 'Z' and resid 85 through 90 removed outlier: 4.797A pdb=" N GLN Z 37 " --> pdb=" O PHE Z 46 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N PHE Z 46 " --> pdb=" O GLN Z 37 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 36 through 39 Processing sheet with id= D, first strand: chain 'A' and resid 63 through 69 Processing sheet with id= E, first strand: chain 'A' and resid 86 through 89 Processing sheet with id= F, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= G, first strand: chain 'A' and resid 107 through 114 removed outlier: 6.327A pdb=" N TYR A 137 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ASN A 110 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS A 139 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N GLU A 112 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL A 141 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS A 114 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY A 143 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR A 216 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LYS A 140 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 218 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N SER A 142 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR A 220 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N THR A 144 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA A 222 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU A 273 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N GLN A 243 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N TRP A 275 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 306 through 309 Processing sheet with id= I, first strand: chain 'Y' and resid 4 through 7 Processing sheet with id= J, first strand: chain 'Y' and resid 85 through 90 removed outlier: 4.797A pdb=" N GLN Y 37 " --> pdb=" O PHE Y 46 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N PHE Y 46 " --> pdb=" O GLN Y 37 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 515 through 520 Processing sheet with id= L, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= M, first strand: chain 'L' and resid 85 through 90 removed outlier: 4.797A pdb=" N GLN L 37 " --> pdb=" O PHE L 46 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N PHE L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 3 through 8 Processing sheet with id= O, first strand: chain 'H' and resid 110 through 112 removed outlier: 3.749A pdb=" N GLY H 50 " --> pdb=" O TRP H 37 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 36 through 39 Processing sheet with id= Q, first strand: chain 'C' and resid 63 through 69 Processing sheet with id= R, first strand: chain 'C' and resid 86 through 89 Processing sheet with id= S, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= T, first strand: chain 'C' and resid 107 through 114 removed outlier: 6.328A pdb=" N TYR C 137 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ASN C 110 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS C 139 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLU C 112 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL C 141 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LYS C 114 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY C 143 " --> pdb=" O LYS C 114 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 216 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LYS C 140 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE C 218 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N SER C 142 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR C 220 " --> pdb=" O SER C 142 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N THR C 144 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA C 222 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU C 273 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLN C 243 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N TRP C 275 " --> pdb=" O GLN C 243 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 306 through 309 Processing sheet with id= V, first strand: chain 'E' and resid 36 through 39 Processing sheet with id= W, first strand: chain 'E' and resid 63 through 69 Processing sheet with id= X, first strand: chain 'E' and resid 86 through 89 Processing sheet with id= Y, first strand: chain 'E' and resid 96 through 98 Processing sheet with id= Z, first strand: chain 'E' and resid 107 through 114 removed outlier: 6.328A pdb=" N TYR E 137 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASN E 110 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS E 139 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLU E 112 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL E 141 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LYS E 114 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY E 143 " --> pdb=" O LYS E 114 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR E 216 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LYS E 140 " --> pdb=" O THR E 216 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE E 218 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N SER E 142 " --> pdb=" O ILE E 218 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR E 220 " --> pdb=" O SER E 142 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N THR E 144 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA E 222 " --> pdb=" O THR E 144 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG E 219 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU E 273 " --> pdb=" O TYR E 241 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N GLN E 243 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TRP E 275 " --> pdb=" O GLN E 243 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 306 through 309 Processing sheet with id= AB, first strand: chain 'F' and resid 515 through 520 Processing sheet with id= AC, first strand: chain 'D' and resid 515 through 520 Processing sheet with id= AD, first strand: chain 'W' and resid 3 through 8 Processing sheet with id= AE, first strand: chain 'W' and resid 110 through 112 removed outlier: 3.749A pdb=" N GLY W 50 " --> pdb=" O TRP W 37 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG W 39 " --> pdb=" O TRP W 48 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N TRP W 48 " --> pdb=" O ARG W 39 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Q' and resid 3 through 8 Processing sheet with id= AG, first strand: chain 'Q' and resid 110 through 112 removed outlier: 3.749A pdb=" N GLY Q 50 " --> pdb=" O TRP Q 37 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG Q 39 " --> pdb=" O TRP Q 48 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N TRP Q 48 " --> pdb=" O ARG Q 39 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 963 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.21 Time building geometry restraints manager: 5.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4568 1.34 - 1.49: 4726 1.49 - 1.64: 5145 1.64 - 1.79: 24 1.79 - 1.94: 24 Bond restraints: 14487 Sorted by residual: bond pdb=" CD1 TYR L 32 " pdb=" CE1 TYR L 32 " ideal model delta sigma weight residual 1.382 1.248 0.134 3.00e-02 1.11e+03 2.00e+01 bond pdb=" CD1 TYR Z 32 " pdb=" CE1 TYR Z 32 " ideal model delta sigma weight residual 1.382 1.248 0.134 3.00e-02 1.11e+03 2.00e+01 bond pdb=" CD1 TYR Y 32 " pdb=" CE1 TYR Y 32 " ideal model delta sigma weight residual 1.382 1.249 0.133 3.00e-02 1.11e+03 1.98e+01 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.86e+01 ... (remaining 14482 not shown) Histogram of bond angle deviations from ideal: 96.71 - 104.46: 270 104.46 - 112.21: 6774 112.21 - 119.96: 6001 119.96 - 127.71: 6425 127.71 - 135.46: 240 Bond angle restraints: 19710 Sorted by residual: angle pdb=" N GLN B 521 " pdb=" CA GLN B 521 " pdb=" C GLN B 521 " ideal model delta sigma weight residual 107.99 119.89 -11.90 1.76e+00 3.23e-01 4.57e+01 angle pdb=" N GLN F 521 " pdb=" CA GLN F 521 " pdb=" C GLN F 521 " ideal model delta sigma weight residual 107.99 119.88 -11.89 1.76e+00 3.23e-01 4.56e+01 angle pdb=" N GLN D 521 " pdb=" CA GLN D 521 " pdb=" C GLN D 521 " ideal model delta sigma weight residual 107.99 119.87 -11.88 1.76e+00 3.23e-01 4.55e+01 angle pdb=" N VAL C 52 " pdb=" CA VAL C 52 " pdb=" C VAL C 52 " ideal model delta sigma weight residual 109.34 96.71 12.63 2.08e+00 2.31e-01 3.68e+01 angle pdb=" N VAL A 52 " pdb=" CA VAL A 52 " pdb=" C VAL A 52 " ideal model delta sigma weight residual 109.34 96.73 12.61 2.08e+00 2.31e-01 3.68e+01 ... (remaining 19705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.21: 7868 20.21 - 40.41: 632 40.41 - 60.61: 134 60.61 - 80.82: 36 80.82 - 101.02: 18 Dihedral angle restraints: 8688 sinusoidal: 3525 harmonic: 5163 Sorted by residual: dihedral pdb=" CA PHE Y 46 " pdb=" C PHE Y 46 " pdb=" N LEU Y 47 " pdb=" CA LEU Y 47 " ideal model delta harmonic sigma weight residual 180.00 149.47 30.53 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA PHE L 46 " pdb=" C PHE L 46 " pdb=" N LEU L 47 " pdb=" CA LEU L 47 " ideal model delta harmonic sigma weight residual 180.00 149.50 30.50 0 5.00e+00 4.00e-02 3.72e+01 dihedral pdb=" CA PHE Z 46 " pdb=" C PHE Z 46 " pdb=" N LEU Z 47 " pdb=" CA LEU Z 47 " ideal model delta harmonic sigma weight residual 180.00 149.50 30.50 0 5.00e+00 4.00e-02 3.72e+01 ... (remaining 8685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1236 0.057 - 0.115: 622 0.115 - 0.172: 253 0.172 - 0.230: 89 0.230 - 0.287: 35 Chirality restraints: 2235 Sorted by residual: chirality pdb=" CB ILE F 610 " pdb=" CA ILE F 610 " pdb=" CG1 ILE F 610 " pdb=" CG2 ILE F 610 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE B 610 " pdb=" CA ILE B 610 " pdb=" CG1 ILE B 610 " pdb=" CG2 ILE B 610 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB ILE D 610 " pdb=" CA ILE D 610 " pdb=" CG1 ILE D 610 " pdb=" CG2 ILE D 610 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 2232 not shown) Planarity restraints: 2523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 274 " 0.022 2.00e-02 2.50e+03 4.40e-02 1.93e+01 pdb=" C ILE E 274 " -0.076 2.00e-02 2.50e+03 pdb=" O ILE E 274 " 0.029 2.00e-02 2.50e+03 pdb=" N TRP E 275 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 274 " -0.022 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C ILE A 274 " 0.076 2.00e-02 2.50e+03 pdb=" O ILE A 274 " -0.029 2.00e-02 2.50e+03 pdb=" N TRP A 275 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 274 " 0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C ILE C 274 " -0.075 2.00e-02 2.50e+03 pdb=" O ILE C 274 " 0.029 2.00e-02 2.50e+03 pdb=" N TRP C 275 " 0.025 2.00e-02 2.50e+03 ... (remaining 2520 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2258 2.76 - 3.29: 12161 3.29 - 3.83: 22227 3.83 - 4.36: 25170 4.36 - 4.90: 45640 Nonbonded interactions: 107456 Sorted by model distance: nonbonded pdb=" O THR B 616 " pdb=" OG1 THR B 620 " model vdw 2.220 2.440 nonbonded pdb=" O THR F 616 " pdb=" OG1 THR F 620 " model vdw 2.220 2.440 nonbonded pdb=" O THR D 616 " pdb=" OG1 THR D 620 " model vdw 2.220 2.440 nonbonded pdb=" OH TYR L 87 " pdb=" O ARG H 44 " model vdw 2.236 2.440 nonbonded pdb=" OG1 THR A 83 " pdb=" OH TYR A 232 " model vdw 2.240 2.440 ... (remaining 107451 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' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'Q' selection = chain 'W' } ncs_group { reference = chain 'L' selection = chain 'Y' selection = chain 'Z' } 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.360 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 38.680 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 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 : 0.015 0.137 14487 Z= 0.950 Angle : 1.667 19.160 19710 Z= 0.889 Chirality : 0.085 0.287 2235 Planarity : 0.011 0.071 2517 Dihedral : 16.533 101.024 5325 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.69 % Favored : 92.80 % Rotamer: Outliers : 3.96 % Allowed : 8.05 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.17), residues: 1749 helix: 0.77 (0.32), residues: 186 sheet: -0.70 (0.21), residues: 498 loop : -2.13 (0.16), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.006 TRP C 104 HIS 0.008 0.003 HIS F 516 PHE 0.058 0.007 PHE C 252 TYR 0.026 0.005 TYR W 54 ARG 0.026 0.003 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 212 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 103 LYS cc_start: 0.6613 (mptt) cc_final: 0.6095 (tttp) REVERT: H 35 TRP cc_start: 0.8165 (m100) cc_final: 0.7484 (m100) REVERT: E 56 LYS cc_start: 0.8316 (mmtp) cc_final: 0.8101 (mmtp) REVERT: W 54 TYR cc_start: 0.6568 (p90) cc_final: 0.6309 (p90) REVERT: Q 54 TYR cc_start: 0.7033 (p90) cc_final: 0.6784 (p90) REVERT: Q 60 TYR cc_start: 0.7694 (m-80) cc_final: 0.7367 (m-80) outliers start: 60 outliers final: 18 residues processed: 267 average time/residue: 0.2713 time to fit residues: 103.7818 Evaluate side-chains 170 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 152 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 627 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 627 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 103 optimal weight: 50.0000 chunk 160 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 93 ASN ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 93 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 61 ASN ** C 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 3 GLN ** Q 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14487 Z= 0.236 Angle : 0.762 11.055 19710 Z= 0.389 Chirality : 0.048 0.178 2235 Planarity : 0.006 0.056 2517 Dihedral : 10.993 100.611 2221 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.66 % Favored : 94.17 % Rotamer: Outliers : 3.04 % Allowed : 13.53 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.18), residues: 1749 helix: 0.87 (0.34), residues: 186 sheet: -0.37 (0.21), residues: 528 loop : -1.96 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 104 HIS 0.006 0.001 HIS D 516 PHE 0.019 0.002 PHE C 252 TYR 0.021 0.002 TYR A 232 ARG 0.005 0.001 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 168 time to evaluate : 1.531 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7777 (mmtp) cc_final: 0.7521 (mmtp) REVERT: A 111 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6381 (mp) REVERT: A 137 TYR cc_start: 0.6685 (m-80) cc_final: 0.6464 (m-80) REVERT: A 163 ASP cc_start: 0.7940 (t70) cc_final: 0.7660 (t0) REVERT: B 548 MET cc_start: 0.6499 (ttt) cc_final: 0.6280 (ttt) REVERT: H 35 TRP cc_start: 0.8075 (m100) cc_final: 0.7474 (m100) REVERT: H 54 TYR cc_start: 0.7433 (p90) cc_final: 0.7015 (p90) REVERT: C 56 LYS cc_start: 0.8198 (mmtp) cc_final: 0.7974 (mmtp) REVERT: D 591 ASP cc_start: 0.7415 (m-30) cc_final: 0.7190 (m-30) REVERT: Q 60 TYR cc_start: 0.7517 (m-80) cc_final: 0.7217 (m-80) outliers start: 46 outliers final: 25 residues processed: 198 average time/residue: 0.2893 time to fit residues: 81.2084 Evaluate side-chains 175 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 93 ASN Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain Y residue 31 THR Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 627 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 627 ILE Chi-restraints excluded: chain W residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 3 GLN ** Q 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14487 Z= 0.341 Angle : 0.795 13.008 19710 Z= 0.396 Chirality : 0.050 0.316 2235 Planarity : 0.006 0.059 2517 Dihedral : 7.793 53.103 2198 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.00 % Favored : 91.82 % Rotamer: Outliers : 3.89 % Allowed : 15.18 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.17), residues: 1749 helix: -0.43 (0.33), residues: 207 sheet: -0.31 (0.21), residues: 480 loop : -2.04 (0.16), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 104 HIS 0.005 0.001 HIS A 39 PHE 0.023 0.002 PHE E 132 TYR 0.027 0.002 TYR W 54 ARG 0.004 0.001 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 151 time to evaluate : 1.468 Fit side-chains REVERT: A 56 LYS cc_start: 0.8108 (mmtp) cc_final: 0.7851 (mmtp) REVERT: A 111 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6704 (mp) REVERT: A 163 ASP cc_start: 0.7977 (t70) cc_final: 0.7744 (t0) REVERT: Y 55 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6485 (tt0) REVERT: C 56 LYS cc_start: 0.8430 (mmtp) cc_final: 0.8145 (mmtp) REVERT: C 162 TYR cc_start: 0.8001 (m-80) cc_final: 0.7620 (m-80) REVERT: E 56 LYS cc_start: 0.8391 (mmtp) cc_final: 0.8039 (mmtm) REVERT: E 84 LYS cc_start: 0.7893 (mttt) cc_final: 0.7650 (mmtp) REVERT: E 136 ARG cc_start: 0.6780 (mpt-90) cc_final: 0.5958 (mmp80) REVERT: F 548 MET cc_start: 0.6915 (tpt) cc_final: 0.6687 (ttt) outliers start: 59 outliers final: 35 residues processed: 197 average time/residue: 0.3009 time to fit residues: 83.4709 Evaluate side-chains 174 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 137 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain Y residue 12 SER Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 83 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 93 ASN ** Y 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN W 3 GLN ** Q 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14487 Z= 0.222 Angle : 0.681 14.958 19710 Z= 0.339 Chirality : 0.047 0.201 2235 Planarity : 0.005 0.055 2517 Dihedral : 6.634 51.714 2190 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.71 % Allowed : 17.36 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.18), residues: 1749 helix: -0.44 (0.33), residues: 207 sheet: -0.58 (0.21), residues: 525 loop : -1.86 (0.17), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 104 HIS 0.002 0.001 HIS F 549 PHE 0.013 0.001 PHE A 132 TYR 0.023 0.002 TYR W 54 ARG 0.006 0.000 ARG D 559 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 144 time to evaluate : 1.604 Fit side-chains REVERT: A 56 LYS cc_start: 0.8059 (mmtp) cc_final: 0.7804 (mmtp) REVERT: A 111 LEU cc_start: 0.6938 (mp) cc_final: 0.6721 (mp) REVERT: A 162 TYR cc_start: 0.8042 (m-80) cc_final: 0.7718 (m-80) REVERT: Y 11 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8148 (mp) REVERT: B 548 MET cc_start: 0.6644 (ttt) cc_final: 0.6431 (ttm) REVERT: C 56 LYS cc_start: 0.8427 (mmtp) cc_final: 0.8148 (mmtp) REVERT: E 56 LYS cc_start: 0.8463 (mmtp) cc_final: 0.8079 (mmtm) REVERT: E 136 ARG cc_start: 0.6672 (mpt-90) cc_final: 0.6269 (mpt180) REVERT: D 548 MET cc_start: 0.6648 (mmm) cc_final: 0.6388 (mtp) REVERT: W 3 GLN cc_start: 0.6731 (mm110) cc_final: 0.6513 (mm110) outliers start: 41 outliers final: 24 residues processed: 173 average time/residue: 0.2647 time to fit residues: 65.9042 Evaluate side-chains 159 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 127 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 145 optimal weight: 0.0070 chunk 118 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 153 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 93 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14487 Z= 0.185 Angle : 0.642 14.849 19710 Z= 0.316 Chirality : 0.045 0.197 2235 Planarity : 0.005 0.054 2517 Dihedral : 6.243 53.305 2189 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.03 % Favored : 92.80 % Rotamer: Outliers : 2.97 % Allowed : 17.36 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.18), residues: 1749 helix: -0.40 (0.34), residues: 207 sheet: -0.42 (0.21), residues: 525 loop : -1.72 (0.17), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP E 104 HIS 0.004 0.000 HIS F 516 PHE 0.010 0.001 PHE E 132 TYR 0.020 0.001 TYR W 54 ARG 0.006 0.000 ARG D 559 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 151 time to evaluate : 1.537 Fit side-chains REVERT: A 111 LEU cc_start: 0.6967 (mp) cc_final: 0.6701 (mp) REVERT: A 162 TYR cc_start: 0.8072 (m-80) cc_final: 0.7763 (m-80) REVERT: Y 55 GLN cc_start: 0.6966 (OUTLIER) cc_final: 0.6418 (tt0) REVERT: Y 79 GLN cc_start: 0.7313 (mp10) cc_final: 0.7027 (mp10) REVERT: C 56 LYS cc_start: 0.8440 (mmtp) cc_final: 0.8188 (mmtp) REVERT: E 56 LYS cc_start: 0.8583 (mmtp) cc_final: 0.8377 (mmtp) REVERT: E 136 ARG cc_start: 0.6438 (mpt-90) cc_final: 0.6167 (mpt-90) outliers start: 45 outliers final: 30 residues processed: 184 average time/residue: 0.2903 time to fit residues: 76.2701 Evaluate side-chains 168 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 50.0000 chunk 154 optimal weight: 50.0000 chunk 33 optimal weight: 10.0000 chunk 100 optimal weight: 50.0000 chunk 42 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14487 Z= 0.403 Angle : 0.769 15.894 19710 Z= 0.379 Chirality : 0.049 0.180 2235 Planarity : 0.006 0.057 2517 Dihedral : 6.777 48.113 2187 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 4.16 % Allowed : 17.43 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.18), residues: 1749 helix: -0.43 (0.33), residues: 207 sheet: -0.34 (0.21), residues: 480 loop : -1.93 (0.16), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 48 HIS 0.004 0.001 HIS A 154 PHE 0.018 0.002 PHE C 132 TYR 0.021 0.002 TYR Z 36 ARG 0.005 0.001 ARG D 596 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 139 time to evaluate : 1.360 Fit side-chains REVERT: A 111 LEU cc_start: 0.7092 (mp) cc_final: 0.6753 (mp) REVERT: Y 55 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6656 (tt0) REVERT: B 596 ARG cc_start: 0.6296 (ttt180) cc_final: 0.6066 (ttt180) REVERT: C 56 LYS cc_start: 0.8463 (mmtp) cc_final: 0.8205 (mmtp) REVERT: E 56 LYS cc_start: 0.8498 (mmtp) cc_final: 0.8231 (mmtp) REVERT: E 136 ARG cc_start: 0.6592 (mpt-90) cc_final: 0.6132 (mpt-90) outliers start: 63 outliers final: 46 residues processed: 184 average time/residue: 0.2789 time to fit residues: 74.1583 Evaluate side-chains 176 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 129 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 83 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 83 PHE Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 72 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 125 optimal weight: 50.0000 chunk 96 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 170 optimal weight: 0.0170 chunk 106 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 GLN ** Q 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14487 Z= 0.238 Angle : 0.669 15.186 19710 Z= 0.331 Chirality : 0.046 0.161 2235 Planarity : 0.005 0.055 2517 Dihedral : 6.350 47.181 2187 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.63 % Allowed : 18.42 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.18), residues: 1749 helix: -0.42 (0.34), residues: 207 sheet: -0.19 (0.22), residues: 486 loop : -1.83 (0.17), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 48 HIS 0.002 0.000 HIS Q 101 PHE 0.012 0.001 PHE E 132 TYR 0.028 0.002 TYR W 54 ARG 0.006 0.000 ARG D 596 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 134 time to evaluate : 1.424 Fit side-chains REVERT: A 111 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6699 (mp) REVERT: Y 55 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6542 (tt0) REVERT: B 596 ARG cc_start: 0.6305 (ttt180) cc_final: 0.6070 (ttt180) REVERT: L 37 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6879 (tt0) REVERT: E 56 LYS cc_start: 0.8554 (mmtp) cc_final: 0.8253 (mmtp) REVERT: E 136 ARG cc_start: 0.6590 (mpt-90) cc_final: 0.6335 (mpt-90) outliers start: 55 outliers final: 46 residues processed: 170 average time/residue: 0.2897 time to fit residues: 71.7480 Evaluate side-chains 182 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 133 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 46 PHE Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 83 PHE Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 72 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 101 optimal weight: 0.2980 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 108 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 93 ASN ** Y 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14487 Z= 0.252 Angle : 0.672 14.998 19710 Z= 0.330 Chirality : 0.046 0.161 2235 Planarity : 0.005 0.055 2517 Dihedral : 6.245 45.953 2187 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.63 % Allowed : 18.28 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.18), residues: 1749 helix: -0.81 (0.32), residues: 225 sheet: -0.07 (0.22), residues: 474 loop : -1.88 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 48 HIS 0.002 0.000 HIS Q 101 PHE 0.012 0.002 PHE E 132 TYR 0.027 0.002 TYR W 54 ARG 0.006 0.000 ARG D 596 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 132 time to evaluate : 1.445 Fit side-chains REVERT: A 111 LEU cc_start: 0.7134 (mp) cc_final: 0.6793 (mp) REVERT: Y 55 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6523 (tt0) REVERT: B 596 ARG cc_start: 0.6335 (ttt180) cc_final: 0.6068 (ttt180) REVERT: L 37 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6867 (tt0) REVERT: H 60 TYR cc_start: 0.7999 (m-80) cc_final: 0.7394 (t80) REVERT: C 56 LYS cc_start: 0.8512 (mmtp) cc_final: 0.8115 (mmtt) REVERT: E 56 LYS cc_start: 0.8513 (mmtp) cc_final: 0.8257 (mmtp) REVERT: E 136 ARG cc_start: 0.6677 (mpt-90) cc_final: 0.6141 (mpt-90) outliers start: 55 outliers final: 50 residues processed: 170 average time/residue: 0.2716 time to fit residues: 66.7143 Evaluate side-chains 182 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 130 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 93 ASN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 46 PHE Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 83 PHE Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 72 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.9672 > 50: distance: 101 - 102: 3.871 distance: 102 - 105: 5.448 distance: 103 - 104: 6.885 distance: 103 - 108: 3.787 distance: 105 - 106: 4.468 distance: 105 - 107: 15.669 distance: 108 - 109: 10.843 distance: 109 - 110: 3.618 distance: 109 - 112: 9.174 distance: 110 - 111: 23.308 distance: 110 - 119: 32.657 distance: 112 - 113: 11.619 distance: 113 - 114: 8.946 distance: 113 - 115: 9.959 distance: 114 - 116: 6.125 distance: 115 - 117: 12.249 distance: 116 - 118: 11.985 distance: 117 - 118: 10.428 distance: 119 - 120: 17.665 distance: 120 - 121: 21.840 distance: 120 - 123: 15.145 distance: 121 - 122: 20.427 distance: 121 - 125: 18.886 distance: 125 - 126: 10.763 distance: 126 - 127: 10.480 distance: 126 - 129: 8.799 distance: 127 - 128: 9.026 distance: 127 - 133: 7.651 distance: 128 - 160: 14.007 distance: 129 - 130: 7.447 distance: 129 - 131: 5.673 distance: 130 - 132: 9.543 distance: 133 - 134: 5.769 distance: 134 - 135: 7.068 distance: 134 - 137: 5.770 distance: 135 - 136: 11.611 distance: 135 - 141: 4.648 distance: 136 - 169: 20.064 distance: 137 - 138: 3.723 distance: 138 - 139: 4.331 distance: 138 - 140: 10.917 distance: 141 - 142: 5.228 distance: 142 - 143: 4.177 distance: 142 - 145: 5.390 distance: 143 - 144: 7.233 distance: 144 - 174: 5.678 distance: 145 - 146: 4.263 distance: 146 - 147: 5.348 distance: 146 - 148: 3.451 distance: 149 - 150: 6.757 distance: 150 - 151: 3.636 distance: 150 - 153: 5.846 distance: 151 - 152: 4.917 distance: 151 - 160: 5.601 distance: 152 - 182: 5.566 distance: 154 - 155: 6.323 distance: 156 - 157: 3.204 distance: 157 - 159: 8.635 distance: 160 - 161: 7.714 distance: 161 - 162: 6.669 distance: 161 - 164: 5.350 distance: 162 - 163: 5.236 distance: 162 - 169: 5.538 distance: 163 - 190: 7.047 distance: 164 - 165: 3.956 distance: 165 - 166: 9.022 distance: 166 - 167: 3.847 distance: 167 - 168: 9.347 distance: 169 - 170: 6.207 distance: 170 - 171: 4.925 distance: 170 - 173: 8.411 distance: 171 - 172: 11.959 distance: 171 - 174: 11.902 distance: 172 - 197: 9.790 distance: 174 - 175: 3.789 distance: 175 - 176: 3.857 distance: 176 - 177: 3.335 distance: 176 - 182: 5.995 distance: 177 - 204: 6.404 distance: 178 - 179: 6.092 distance: 179 - 181: 6.718