Starting phenix.real_space_refine (version: dev) on Tue Feb 28 07:46:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8diu_27443/02_2023/8diu_27443.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8diu_27443/02_2023/8diu_27443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8diu_27443/02_2023/8diu_27443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8diu_27443/02_2023/8diu_27443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8diu_27443/02_2023/8diu_27443.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8diu_27443/02_2023/8diu_27443.pdb" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 1.000 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 15044 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "D TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 52": "OD1" <-> "OD2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 291": "OE1" <-> "OE2" Residue "D ASP 293": "OD1" <-> "OD2" Residue "D GLU 401": "OE1" <-> "OE2" Residue "D PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ASP 204": "OD1" <-> "OD2" Residue "A TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 494": "OE1" <-> "OE2" Residue "G GLU 6": "OE1" <-> "OE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ASP 74": "OD1" <-> "OD2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ASP 74": "OD1" <-> "OD2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C ASP 93": "OD1" <-> "OD2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 51": "OD1" <-> "OD2" Residue "F ASP 61": "OD1" <-> "OD2" Residue "F ASP 93": "OD1" <-> "OD2" Residue "F TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 61": "OD1" <-> "OD2" Residue "I ASP 93": "OD1" <-> "OD2" Residue "I TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 17228 Number of models: 1 Model: "" Number of chains: 23 Chain: "D" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3853 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3853 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3853 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 895 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 895 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 895 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 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: 1 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "L" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 9.50, per 1000 atoms: 0.55 Number of scatterers: 17228 At special positions: 0 Unit cell: (128.25, 135.675, 145.8, 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 81 16.00 O 3539 8.00 N 2853 7.00 C 10755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 481 " distance=2.03 Simple disulfide: pdb=" SG CYS D 59 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 84 " distance=2.03 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS D 488 " - pdb=" SG CYS D 492 " distance=2.03 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 481 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 488 " - pdb=" SG CYS A 492 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 481 " distance=2.03 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 84 " distance=2.03 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 488 " - pdb=" SG CYS B 492 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 89 " 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 BETA1-4 " 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 N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 28 " " NAG A 602 " - " ASN A 40 " " NAG A 603 " - " ASN A 71 " " NAG A 604 " - " ASN A 142 " " NAG A 605 " - " ASN A 177 " " NAG A 606 " - " ASN A 286 " " NAG A 607 " - " ASN A 498 " " NAG B 601 " - " ASN B 28 " " NAG B 602 " - " ASN B 40 " " NAG B 603 " - " ASN B 71 " " NAG B 604 " - " ASN B 142 " " NAG B 605 " - " ASN B 177 " " NAG B 606 " - " ASN B 286 " " NAG B 607 " - " ASN B 498 " " NAG D 601 " - " ASN D 28 " " NAG D 602 " - " ASN D 40 " " NAG D 603 " - " ASN D 71 " " NAG D 604 " - " ASN D 142 " " NAG D 605 " - " ASN D 177 " " NAG D 606 " - " ASN D 286 " " NAG D 607 " - " ASN D 498 " " NAG J 1 " - " ASN D 104 " " NAG K 1 " - " ASN D 304 " " NAG L 1 " - " ASN A 104 " " NAG M 1 " - " ASN A 304 " " NAG N 1 " - " ASN B 104 " " NAG O 1 " - " ASN B 304 " Time building additional restraints: 6.59 Conformation dependent library (CDL) restraints added in 2.5 seconds 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 51 sheets defined 18.5% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'D' and resid 73 through 80 Processing helix chain 'D' and resid 81 through 89 removed outlier: 4.057A pdb=" N GLU D 85 " --> pdb=" O PRO D 82 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N SER D 86 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE D 88 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER D 89 " --> pdb=" O SER D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 123 Processing helix chain 'D' and resid 201 through 210 Processing helix chain 'D' and resid 381 through 403 removed outlier: 3.502A pdb=" N THR D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 471 removed outlier: 3.759A pdb=" N GLU D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU D 452 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP D 453 " --> pdb=" O GLU D 449 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN D 469 " --> pdb=" O LYS D 465 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 470 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.647A pdb=" N PHE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 201 through 210 Processing helix chain 'A' and resid 381 through 403 removed outlier: 3.513A pdb=" N THR A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 471 removed outlier: 3.749A pdb=" N GLU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 452 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 84 through 89 removed outlier: 3.637A pdb=" N PHE B 88 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER B 89 " --> pdb=" O SER B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 123 Processing helix chain 'B' and resid 201 through 210 Processing helix chain 'B' and resid 381 through 403 removed outlier: 3.749A pdb=" N MET B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 471 removed outlier: 3.763A pdb=" N GLU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU B 452 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 469 " --> pdb=" O LYS B 465 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 470 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.779A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.861A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.912A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.573A pdb=" N GLU I 84 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 375 through 380 Processing sheet with id=AA2, first strand: chain 'D' and resid 31 through 32 removed outlier: 4.621A pdb=" N ASP D 31 " --> pdb=" O VAL D 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 46 through 48 Processing sheet with id=AA4, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AA5, first strand: chain 'D' and resid 57 through 61 removed outlier: 5.166A pdb=" N ARG D 60 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N CYS D 292 " --> pdb=" O ARG D 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 67 through 68 removed outlier: 6.535A pdb=" N LEU D 67 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE D 96 " --> pdb=" O ILE D 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 125 through 132 removed outlier: 7.055A pdb=" N SER D 275 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE D 128 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA D 273 " --> pdb=" O PHE D 128 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG D 130 " --> pdb=" O ALA D 271 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA D 271 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR D 270 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU D 193 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LEU D 193 " --> pdb=" O PRO D 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 125 through 132 removed outlier: 7.055A pdb=" N SER D 275 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE D 128 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA D 273 " --> pdb=" O PHE D 128 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG D 130 " --> pdb=" O ALA D 271 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA D 271 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR D 270 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU D 193 " --> pdb=" O TYR D 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 150 through 155 removed outlier: 4.766A pdb=" N CYS D 153 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER D 160 " --> pdb=" O CYS D 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 178 through 183 removed outlier: 3.510A pdb=" N LEU D 178 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 302 through 303 removed outlier: 3.501A pdb=" N CYS D 296 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 375 through 380 Processing sheet with id=AB4, first strand: chain 'A' and resid 31 through 32 removed outlier: 4.602A pdb=" N ASP A 31 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AB6, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AB7, first strand: chain 'A' and resid 57 through 61 removed outlier: 5.117A pdb=" N ARG A 60 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS A 292 " --> pdb=" O ARG A 60 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.546A pdb=" N LEU A 67 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE A 96 " --> pdb=" O ILE A 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 125 through 132 removed outlier: 7.066A pdb=" N SER A 275 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE A 128 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA A 273 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG A 130 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA A 271 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR A 270 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU A 193 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU A 193 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 125 through 132 removed outlier: 7.066A pdb=" N SER A 275 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE A 128 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA A 273 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG A 130 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA A 271 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR A 270 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU A 193 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 150 through 155 removed outlier: 4.761A pdb=" N CYS A 153 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 160 " --> pdb=" O CYS A 153 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 178 through 183 removed outlier: 3.505A pdb=" N ALA A 261 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 302 through 303 removed outlier: 3.633A pdb=" N CYS A 296 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 375 through 380 Processing sheet with id=AC6, first strand: chain 'B' and resid 31 through 32 removed outlier: 4.617A pdb=" N ASP B 31 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 46 through 48 Processing sheet with id=AC8, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AC9, first strand: chain 'B' and resid 57 through 61 removed outlier: 5.207A pdb=" N ARG B 60 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N CYS B 292 " --> pdb=" O ARG B 60 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 67 through 68 removed outlier: 6.550A pdb=" N LEU B 67 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 96 " --> pdb=" O ILE B 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 125 through 132 removed outlier: 7.063A pdb=" N SER B 275 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE B 128 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA B 273 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG B 130 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 271 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR B 270 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU B 193 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU B 193 " --> pdb=" O PRO B 268 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 125 through 132 removed outlier: 7.063A pdb=" N SER B 275 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE B 128 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA B 273 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG B 130 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 271 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR B 270 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU B 193 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 150 through 155 removed outlier: 4.762A pdb=" N CYS B 153 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 160 " --> pdb=" O CYS B 153 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AD6, first strand: chain 'B' and resid 302 through 303 removed outlier: 3.506A pdb=" N CYS B 296 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AD8, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.679A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.895A pdb=" N VAL G 110 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.658A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.910A pdb=" N VAL E 110 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.738A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.918A pdb=" N VAL H 110 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.760A pdb=" N VAL C 10 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.760A pdb=" N VAL C 10 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 18 through 22 Processing sheet with id=AF1, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.749A pdb=" N VAL F 10 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.749A pdb=" N VAL F 10 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 18 through 22 Processing sheet with id=AF4, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.786A pdb=" N VAL I 10 " --> pdb=" O THR I 109 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.786A pdb=" N VAL I 10 " --> pdb=" O THR I 109 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 18 through 22 653 hydrogen bonds defined for protein. 1710 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.90 Time building geometry restraints manager: 7.14 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: 5478 1.34 - 1.47: 4467 1.47 - 1.59: 7434 1.59 - 1.71: 0 1.71 - 1.83: 114 Bond restraints: 17493 Sorted by residual: bond pdb=" C1 NAG B 603 " pdb=" C2 NAG B 603 " ideal model delta sigma weight residual 1.526 1.556 -0.030 2.00e-02 2.50e+03 2.23e+00 bond pdb=" C TYR A 503 " pdb=" N PRO A 504 " ideal model delta sigma weight residual 1.334 1.354 -0.019 1.51e-02 4.39e+03 1.65e+00 bond pdb=" CB ASN B 104 " pdb=" CG ASN B 104 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.62e+00 bond pdb=" CB ASN D 104 " pdb=" CG ASN D 104 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.49e+00 bond pdb=" C ARG F 95 " pdb=" N PRO F 96 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.25e+00 ... (remaining 17488 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.10: 562 107.10 - 113.83: 9694 113.83 - 120.56: 6410 120.56 - 127.30: 6880 127.30 - 134.03: 214 Bond angle restraints: 23760 Sorted by residual: angle pdb=" N ASN D 104 " pdb=" CA ASN D 104 " pdb=" C ASN D 104 " ideal model delta sigma weight residual 108.02 114.86 -6.84 1.75e+00 3.27e-01 1.53e+01 angle pdb=" C ASN A 142 " pdb=" N HIS A 143 " pdb=" CA HIS A 143 " ideal model delta sigma weight residual 121.54 128.83 -7.29 1.91e+00 2.74e-01 1.46e+01 angle pdb=" C ASN D 142 " pdb=" N HIS D 143 " pdb=" CA HIS D 143 " ideal model delta sigma weight residual 121.54 128.80 -7.26 1.91e+00 2.74e-01 1.44e+01 angle pdb=" C ASN B 142 " pdb=" N HIS B 143 " pdb=" CA HIS B 143 " ideal model delta sigma weight residual 121.54 128.73 -7.19 1.91e+00 2.74e-01 1.42e+01 angle pdb=" C ASP C 51 " pdb=" N ASN C 52 " pdb=" CA ASN C 52 " ideal model delta sigma weight residual 121.54 126.79 -5.25 1.91e+00 2.74e-01 7.56e+00 ... (remaining 23755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 8724 16.35 - 32.71: 1036 32.71 - 49.06: 367 49.06 - 65.41: 111 65.41 - 81.77: 28 Dihedral angle restraints: 10266 sinusoidal: 4119 harmonic: 6147 Sorted by residual: dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS A 292 " pdb=" CB CYS A 292 " ideal model delta sinusoidal sigma weight residual -86.00 -19.35 -66.65 1 1.00e+01 1.00e-02 5.80e+01 dihedral pdb=" CB CYS D 59 " pdb=" SG CYS D 59 " pdb=" SG CYS D 292 " pdb=" CB CYS D 292 " ideal model delta sinusoidal sigma weight residual -86.00 -21.43 -64.57 1 1.00e+01 1.00e-02 5.48e+01 dihedral pdb=" CA ILE D 303 " pdb=" C ILE D 303 " pdb=" N ASN D 304 " pdb=" CA ASN D 304 " ideal model delta harmonic sigma weight residual 180.00 147.60 32.40 0 5.00e+00 4.00e-02 4.20e+01 ... (remaining 10263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2210 0.059 - 0.119: 427 0.119 - 0.178: 29 0.178 - 0.237: 2 0.237 - 0.297: 2 Chirality restraints: 2670 Sorted by residual: chirality pdb=" CA ASN D 104 " pdb=" N ASN D 104 " pdb=" C ASN D 104 " pdb=" CB ASN D 104 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN D 104 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C1 NAG D 601 " pdb=" ND2 ASN D 28 " pdb=" C2 NAG D 601 " pdb=" O5 NAG D 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.93e-01 ... (remaining 2667 not shown) Planarity restraints: 3057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 503 " 0.057 5.00e-02 4.00e+02 8.60e-02 1.18e+01 pdb=" N PRO A 504 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 504 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 504 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 104 " -0.027 2.00e-02 2.50e+03 2.53e-02 8.01e+00 pdb=" CG ASN B 104 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 104 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 104 " 0.032 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 177 " 0.021 2.00e-02 2.50e+03 1.91e-02 4.54e+00 pdb=" CG ASN A 177 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 177 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 177 " -0.019 2.00e-02 2.50e+03 pdb=" C1 NAG A 605 " 0.020 2.00e-02 2.50e+03 ... (remaining 3054 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3398 2.78 - 3.31: 13857 3.31 - 3.84: 27069 3.84 - 4.37: 33657 4.37 - 4.90: 58903 Nonbonded interactions: 136884 Sorted by model distance: nonbonded pdb=" OD1 ASN B 472 " pdb=" OH TYR B 503 " model vdw 2.248 2.440 nonbonded pdb=" OD1 ASN D 472 " pdb=" OH TYR D 503 " model vdw 2.249 2.440 nonbonded pdb=" OD1 ASN B 71 " pdb=" N2 NAG B 603 " model vdw 2.252 2.520 nonbonded pdb=" O LYS G 13 " pdb=" OG SER G 16 " model vdw 2.258 2.440 nonbonded pdb=" OD1 ASP A 453 " pdb=" O HOH A 701 " model vdw 2.259 2.440 ... (remaining 136879 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 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 10755 2.51 5 N 2853 2.21 5 O 3539 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 9.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.020 Extract box with map and model: 36.880 Check model and map are aligned: 0.260 Process input model: 45.670 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.150 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:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.004 0.044 17493 Z= 0.239 Angle : 0.642 8.979 23760 Z= 0.352 Chirality : 0.046 0.297 2670 Planarity : 0.005 0.086 3030 Dihedral : 17.093 81.767 6297 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.15 % Favored : 96.43 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.02 (0.17), residues: 2127 helix: 2.04 (0.29), residues: 345 sheet: 0.91 (0.21), residues: 615 loop : -1.17 (0.16), residues: 1167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 151 time to evaluate : 1.996 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 55 residues processed: 207 average time/residue: 1.1485 time to fit residues: 270.8510 Evaluate side-chains 197 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 142 time to evaluate : 2.215 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 51 residues processed: 4 average time/residue: 0.1537 time to fit residues: 3.8604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.9980 chunk 156 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 162 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 201 ASN D 404 ASN D 469 GLN A 201 ASN A 469 GLN B 201 ASN B 469 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.0403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 17493 Z= 0.209 Angle : 0.593 8.544 23760 Z= 0.317 Chirality : 0.045 0.322 2670 Planarity : 0.005 0.060 3030 Dihedral : 5.002 43.560 2541 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.87 % Favored : 96.71 % Rotamer Outliers : 6.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.18), residues: 2127 helix: 2.20 (0.29), residues: 351 sheet: 1.03 (0.21), residues: 615 loop : -1.04 (0.17), residues: 1161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 154 time to evaluate : 2.021 Fit side-chains revert: symmetry clash outliers start: 113 outliers final: 75 residues processed: 237 average time/residue: 1.1114 time to fit residues: 300.6902 Evaluate side-chains 222 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 147 time to evaluate : 2.008 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 58 residues processed: 17 average time/residue: 0.6197 time to fit residues: 15.6345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 203 optimal weight: 20.0000 chunk 167 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 404 ASN D 469 GLN A 472 ASN B 201 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.0561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 17493 Z= 0.242 Angle : 0.600 8.830 23760 Z= 0.321 Chirality : 0.046 0.471 2670 Planarity : 0.005 0.051 3030 Dihedral : 4.994 44.765 2541 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.01 % Favored : 96.57 % Rotamer Outliers : 6.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.18), residues: 2127 helix: 2.19 (0.29), residues: 354 sheet: 1.10 (0.20), residues: 615 loop : -1.02 (0.17), residues: 1158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 151 time to evaluate : 1.915 Fit side-chains revert: symmetry clash outliers start: 109 outliers final: 72 residues processed: 228 average time/residue: 1.1397 time to fit residues: 295.0857 Evaluate side-chains 222 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 150 time to evaluate : 1.807 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 58 residues processed: 15 average time/residue: 0.5829 time to fit residues: 13.5571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 188 optimal weight: 20.0000 chunk 200 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 179 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 201 ASN D 404 ASN D 469 GLN B 469 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 17493 Z= 0.286 Angle : 0.630 8.829 23760 Z= 0.338 Chirality : 0.047 0.497 2670 Planarity : 0.005 0.046 3030 Dihedral : 5.050 43.290 2541 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.15 % Favored : 96.43 % Rotamer Outliers : 6.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.18), residues: 2127 helix: 2.14 (0.29), residues: 354 sheet: 1.18 (0.20), residues: 603 loop : -1.07 (0.17), residues: 1170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 150 time to evaluate : 2.075 Fit side-chains revert: symmetry clash outliers start: 116 outliers final: 71 residues processed: 238 average time/residue: 1.0727 time to fit residues: 292.8866 Evaluate side-chains 217 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 146 time to evaluate : 2.029 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 60 residues processed: 12 average time/residue: 0.6425 time to fit residues: 12.2869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 404 ASN D 469 GLN B 469 GLN F 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 17493 Z= 0.179 Angle : 0.541 8.269 23760 Z= 0.290 Chirality : 0.044 0.456 2670 Planarity : 0.004 0.042 3030 Dihedral : 4.865 42.871 2541 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.73 % Favored : 96.85 % Rotamer Outliers : 5.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.18), residues: 2127 helix: 2.39 (0.28), residues: 351 sheet: 1.24 (0.20), residues: 600 loop : -0.98 (0.17), residues: 1176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 157 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 66 residues processed: 227 average time/residue: 1.1398 time to fit residues: 294.7684 Evaluate side-chains 212 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 146 time to evaluate : 2.030 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 60 residues processed: 7 average time/residue: 0.3607 time to fit residues: 6.2005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 39 optimal weight: 0.0070 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 382 GLN D 404 ASN D 469 GLN B 469 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 17493 Z= 0.334 Angle : 0.653 9.126 23760 Z= 0.350 Chirality : 0.049 0.499 2670 Planarity : 0.005 0.047 3030 Dihedral : 5.067 41.634 2541 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.87 % Favored : 96.71 % Rotamer Outliers : 5.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.18), residues: 2127 helix: 2.12 (0.29), residues: 354 sheet: 1.24 (0.20), residues: 603 loop : -1.03 (0.17), residues: 1170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 154 time to evaluate : 2.144 Fit side-chains revert: symmetry clash outliers start: 104 outliers final: 76 residues processed: 237 average time/residue: 1.0943 time to fit residues: 299.3690 Evaluate side-chains 224 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 148 time to evaluate : 2.188 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 65 residues processed: 12 average time/residue: 0.5570 time to fit residues: 11.4974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 199 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 382 GLN D 404 ASN D 469 GLN A 469 GLN B 469 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 17493 Z= 0.161 Angle : 0.521 7.840 23760 Z= 0.279 Chirality : 0.044 0.449 2670 Planarity : 0.004 0.041 3030 Dihedral : 4.772 41.580 2541 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.63 % Favored : 96.94 % Rotamer Outliers : 4.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 2127 helix: 2.42 (0.28), residues: 351 sheet: 1.31 (0.20), residues: 600 loop : -0.94 (0.17), residues: 1176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 152 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 68 residues processed: 221 average time/residue: 1.1544 time to fit residues: 290.8537 Evaluate side-chains 215 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 147 time to evaluate : 1.958 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 60 residues processed: 9 average time/residue: 0.3437 time to fit residues: 7.0267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 60 optimal weight: 0.0170 chunk 39 optimal weight: 0.0170 chunk 38 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 chunk 135 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 382 GLN D 404 ASN D 469 GLN A 469 GLN B 469 GLN I 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 17493 Z= 0.135 Angle : 0.495 7.298 23760 Z= 0.265 Chirality : 0.044 0.433 2670 Planarity : 0.004 0.038 3030 Dihedral : 4.609 41.337 2541 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.82 % Favored : 96.76 % Rotamer Outliers : 4.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2127 helix: 2.69 (0.28), residues: 348 sheet: 1.37 (0.20), residues: 600 loop : -0.87 (0.17), residues: 1179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 153 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 61 residues processed: 220 average time/residue: 1.1720 time to fit residues: 293.0050 Evaluate side-chains 208 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 147 time to evaluate : 1.943 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 57 residues processed: 5 average time/residue: 0.1832 time to fit residues: 4.0548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 382 GLN D 404 ASN D 469 GLN A 469 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN C 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 17493 Z= 0.359 Angle : 0.666 8.547 23760 Z= 0.357 Chirality : 0.051 0.588 2670 Planarity : 0.005 0.044 3030 Dihedral : 5.030 39.961 2541 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.06 % Favored : 96.52 % Rotamer Outliers : 4.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.18), residues: 2127 helix: 2.16 (0.29), residues: 354 sheet: 1.35 (0.20), residues: 603 loop : -0.99 (0.17), residues: 1170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 149 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 65 residues processed: 219 average time/residue: 1.1786 time to fit residues: 294.9818 Evaluate side-chains 209 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 144 time to evaluate : 2.371 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 57 residues processed: 9 average time/residue: 0.4965 time to fit residues: 8.7031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 0.9980 chunk 119 optimal weight: 0.0270 chunk 93 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 382 GLN D 404 ASN D 469 GLN A 469 GLN B 469 GLN C 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 17493 Z= 0.194 Angle : 0.549 7.978 23760 Z= 0.295 Chirality : 0.046 0.533 2670 Planarity : 0.004 0.041 3030 Dihedral : 4.852 39.391 2541 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.87 % Favored : 96.76 % Rotamer Outliers : 3.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.49 (0.18), residues: 2127 helix: 2.36 (0.28), residues: 351 sheet: 1.39 (0.20), residues: 600 loop : -0.95 (0.17), residues: 1176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 145 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 63 residues processed: 203 average time/residue: 1.1983 time to fit residues: 276.2350 Evaluate side-chains 205 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 142 time to evaluate : 2.203 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 58 residues processed: 6 average time/residue: 0.2159 time to fit residues: 4.9437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 382 GLN D 404 ASN D 469 GLN A 469 GLN B 469 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.140715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097393 restraints weight = 20602.021| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.19 r_work: 0.3139 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 17493 Z= 0.225 Angle : 0.573 7.789 23760 Z= 0.308 Chirality : 0.047 0.537 2670 Planarity : 0.004 0.043 3030 Dihedral : 4.859 37.885 2541 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.24 % Favored : 96.47 % Rotamer Outliers : 3.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.50 (0.18), residues: 2127 helix: 2.43 (0.28), residues: 348 sheet: 1.41 (0.20), residues: 600 loop : -0.97 (0.17), residues: 1179 =============================================================================== Job complete usr+sys time: 5975.52 seconds wall clock time: 108 minutes 18.17 seconds (6498.17 seconds total)