Starting phenix.real_space_refine on Fri Mar 22 04:04:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8diu_27443/03_2024/8diu_27443.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8diu_27443/03_2024/8diu_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_27443/03_2024/8diu_27443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8diu_27443/03_2024/8diu_27443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8diu_27443/03_2024/8diu_27443.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8diu_27443/03_2024/8diu_27443.pdb" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9 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 dihedrals: 6 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: 9 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 dihedrals: 6 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: 9 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 dihedrals: 6 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 dihedrals: 21 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 dihedrals: 21 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 dihedrals: 21 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: 9.77, per 1000 atoms: 0.57 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: 6.82 Conformation dependent library (CDL) restraints added in 3.4 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: 2.54 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: 6.71 Time building geometry restraints manager: 7.37 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 J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.44e+00 bond pdb=" C1 NAG B 603 " pdb=" O5 NAG B 603 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.83e+00 bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.10e+00 bond pdb=" C1 BMA N 3 " pdb=" C2 BMA N 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.00e+00 bond pdb=" C1 NAG B 606 " pdb=" O5 NAG B 606 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.84e+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 - 21.78: 9582 21.78 - 43.57: 864 43.57 - 65.35: 284 65.35 - 87.14: 46 87.14 - 108.92: 12 Dihedral angle restraints: 10788 sinusoidal: 4641 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 10785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2170 0.059 - 0.119: 462 0.119 - 0.178: 31 0.178 - 0.237: 2 0.237 - 0.297: 5 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=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 ... (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 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: 7.610 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: 0.010 Extract box with map and model: 36.050 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 50.430 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 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 0.047 17493 Z= 0.278 Angle : 0.693 8.979 23760 Z= 0.359 Chirality : 0.048 0.297 2670 Planarity : 0.005 0.086 3030 Dihedral : 18.251 108.920 6819 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 % Allowed : 24.03 % Favored : 72.44 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 92 HIS 0.005 0.001 HIS A 25 PHE 0.016 0.002 PHE B 128 TYR 0.013 0.001 TYR F 99 ARG 0.006 0.000 ARG B 325 *********************** 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 : 1.943 Fit side-chains revert: symmetry clash REVERT: B 295 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.7977 (ptmt) REVERT: C 32 ASP cc_start: 0.6601 (OUTLIER) cc_final: 0.6246 (m-30) REVERT: F 32 ASP cc_start: 0.6655 (OUTLIER) cc_final: 0.6138 (m-30) REVERT: I 32 ASP cc_start: 0.6544 (OUTLIER) cc_final: 0.6120 (m-30) outliers start: 63 outliers final: 55 residues processed: 207 average time/residue: 1.1034 time to fit residues: 259.2066 Evaluate side-chains 199 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 140 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 492 CYS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 492 CYS Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 28 ASN Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 73 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.9990 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: 3.9990 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 371 GLN A 469 GLN B 201 ASN B 469 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.0474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17493 Z= 0.203 Angle : 0.612 8.839 23760 Z= 0.314 Chirality : 0.045 0.252 2670 Planarity : 0.005 0.059 3030 Dihedral : 10.861 68.726 3150 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.87 % Favored : 96.71 % Rotamer: Outliers : 5.38 % Allowed : 21.29 % Favored : 73.33 % 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: 0.25 (0.18), residues: 2127 helix: 2.16 (0.28), residues: 354 sheet: 1.03 (0.20), residues: 615 loop : -1.01 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS A 25 PHE 0.016 0.002 PHE D 128 TYR 0.021 0.001 TYR I 99 ARG 0.003 0.000 ARG B 325 *********************** 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 245 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 149 time to evaluate : 1.998 Fit side-chains revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8314 (mp) REVERT: D 187 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: D 293 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8122 (m-30) REVERT: D 371 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7800 (tp40) REVERT: A 187 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: B 465 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7731 (ttmt) REVERT: I 32 ASP cc_start: 0.6543 (OUTLIER) cc_final: 0.6112 (m-30) outliers start: 96 outliers final: 59 residues processed: 213 average time/residue: 1.1492 time to fit residues: 276.6482 Evaluate side-chains 205 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 139 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 371 GLN Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 371 GLN Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 28 ASN Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 3.9990 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: 0.0770 chunk 203 optimal weight: 20.0000 chunk 167 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- 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 371 GLN A 472 ASN B 201 ASN B 469 GLN C 28 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17493 Z= 0.273 Angle : 0.651 8.960 23760 Z= 0.337 Chirality : 0.047 0.391 2670 Planarity : 0.005 0.050 3030 Dihedral : 9.579 59.311 3116 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.01 % Favored : 96.57 % Rotamer: Outliers : 5.60 % Allowed : 21.06 % Favored : 73.33 % 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: 0.25 (0.18), residues: 2127 helix: 2.14 (0.29), residues: 354 sheet: 1.15 (0.20), residues: 600 loop : -1.05 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.007 0.001 HIS D 25 PHE 0.017 0.002 PHE D 128 TYR 0.017 0.002 TYR I 99 ARG 0.003 0.000 ARG E 30 *********************** 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 250 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 150 time to evaluate : 1.908 Fit side-chains revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8395 (mp) REVERT: D 187 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: D 449 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: A 187 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: A 449 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: B 187 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: B 465 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7833 (ttmt) REVERT: G 100 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8188 (mtt) REVERT: C 74 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6926 (tm) REVERT: C 111 LEU cc_start: 0.3661 (OUTLIER) cc_final: 0.3010 (pp) REVERT: F 32 ASP cc_start: 0.6540 (OUTLIER) cc_final: 0.5981 (m-30) REVERT: I 32 ASP cc_start: 0.6559 (OUTLIER) cc_final: 0.6131 (m-30) outliers start: 100 outliers final: 54 residues processed: 218 average time/residue: 1.1579 time to fit residues: 284.7042 Evaluate side-chains 213 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 147 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR 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: 3.9990 chunk 126 optimal weight: 3.9990 chunk 188 optimal weight: 0.0570 chunk 200 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 179 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 201 ASN D 382 GLN D 404 ASN D 469 GLN B 201 ASN B 469 GLN I 28 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0796 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= 0.283 Angle : 0.652 8.779 23760 Z= 0.339 Chirality : 0.048 0.394 2670 Planarity : 0.005 0.046 3030 Dihedral : 8.617 57.252 3105 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.15 % Favored : 96.43 % Rotamer: Outliers : 5.88 % Allowed : 20.50 % Favored : 73.61 % 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: 0.24 (0.18), residues: 2127 helix: 2.10 (0.28), residues: 354 sheet: 1.17 (0.20), residues: 603 loop : -1.07 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.007 0.001 HIS D 25 PHE 0.017 0.002 PHE A 128 TYR 0.015 0.002 TYR I 99 ARG 0.003 0.000 ARG E 30 *********************** 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 253 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 148 time to evaluate : 2.047 Fit side-chains revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8392 (mp) REVERT: D 187 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: D 449 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: D 502 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7893 (t70) REVERT: A 22 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8676 (mt) REVERT: A 187 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: A 449 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: A 465 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7803 (ttmt) REVERT: B 22 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8774 (mt) REVERT: B 37 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8602 (mp) REVERT: B 187 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: B 465 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7865 (ttmt) REVERT: C 111 LEU cc_start: 0.4037 (OUTLIER) cc_final: 0.3390 (pp) REVERT: F 68 SER cc_start: 0.7195 (p) cc_final: 0.6587 (m) outliers start: 105 outliers final: 57 residues processed: 223 average time/residue: 1.0853 time to fit residues: 275.3830 Evaluate side-chains 214 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 144 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR 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: 0.7980 chunk 2 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 201 ASN D 382 GLN D 404 ASN D 469 GLN A 371 GLN A 469 GLN B 469 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17493 Z= 0.227 Angle : 0.602 8.568 23760 Z= 0.313 Chirality : 0.046 0.382 2670 Planarity : 0.005 0.044 3030 Dihedral : 8.035 57.511 3105 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.10 % Favored : 96.47 % Rotamer: Outliers : 5.15 % Allowed : 21.01 % Favored : 73.84 % 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: 0.34 (0.18), residues: 2127 helix: 2.33 (0.28), residues: 348 sheet: 1.24 (0.20), residues: 600 loop : -1.04 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.006 0.001 HIS D 25 PHE 0.016 0.002 PHE D 128 TYR 0.013 0.001 TYR G 95 ARG 0.002 0.000 ARG E 30 *********************** 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 243 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 151 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8337 (mp) REVERT: D 187 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: D 502 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7862 (t70) REVERT: A 187 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: A 465 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7997 (ttmt) REVERT: B 37 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8602 (mp) REVERT: B 187 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: B 465 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7749 (ttmt) REVERT: C 111 LEU cc_start: 0.4299 (OUTLIER) cc_final: 0.3678 (pp) REVERT: F 68 SER cc_start: 0.7190 (p) cc_final: 0.6606 (m) outliers start: 92 outliers final: 54 residues processed: 215 average time/residue: 1.1523 time to fit residues: 280.4846 Evaluate side-chains 211 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 148 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 371 GLN Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR 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: 5.9990 chunk 39 optimal weight: 0.0980 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 200 optimal weight: 20.0000 chunk 166 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 201 ASN D 382 GLN D 404 ASN D 469 GLN A 371 GLN B 469 GLN C 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0904 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= 0.281 Angle : 0.643 8.744 23760 Z= 0.334 Chirality : 0.047 0.380 2670 Planarity : 0.005 0.046 3030 Dihedral : 7.803 58.803 3096 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.10 % Favored : 96.47 % Rotamer: Outliers : 5.88 % Allowed : 20.62 % Favored : 73.50 % 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: 0.30 (0.18), residues: 2127 helix: 2.21 (0.28), residues: 351 sheet: 1.25 (0.20), residues: 600 loop : -1.06 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.008 0.001 HIS D 25 PHE 0.017 0.002 PHE D 128 TYR 0.014 0.002 TYR H 95 ARG 0.002 0.000 ARG D 238 *********************** 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 256 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 151 time to evaluate : 2.106 Fit side-chains revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8365 (mp) REVERT: D 187 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: D 266 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8307 (mt) REVERT: D 449 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: D 502 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7882 (t70) REVERT: A 22 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8703 (mt) REVERT: A 37 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8565 (mp) REVERT: A 187 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: A 465 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.8013 (ttmt) REVERT: B 22 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8727 (mt) REVERT: B 37 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8607 (mp) REVERT: B 187 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: B 465 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7851 (ttmt) REVERT: C 111 LEU cc_start: 0.4280 (OUTLIER) cc_final: 0.3650 (pp) REVERT: F 68 SER cc_start: 0.7165 (p) cc_final: 0.6565 (m) REVERT: I 107 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7618 (tttp) outliers start: 105 outliers final: 66 residues processed: 230 average time/residue: 1.0753 time to fit residues: 281.1164 Evaluate side-chains 229 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 148 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 107 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 199 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 201 ASN D 382 GLN D 404 ASN D 469 GLN A 469 GLN B 469 GLN F 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17493 Z= 0.299 Angle : 0.662 8.757 23760 Z= 0.344 Chirality : 0.048 0.400 2670 Planarity : 0.005 0.047 3030 Dihedral : 7.753 59.709 3096 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.96 % Favored : 96.61 % Rotamer: Outliers : 5.88 % Allowed : 20.50 % Favored : 73.61 % 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: 0.27 (0.18), residues: 2127 helix: 2.15 (0.28), residues: 351 sheet: 1.25 (0.20), residues: 603 loop : -1.08 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 93 HIS 0.008 0.001 HIS D 25 PHE 0.017 0.002 PHE D 128 TYR 0.014 0.002 TYR H 95 ARG 0.002 0.000 ARG D 238 *********************** 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 256 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 151 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8388 (mp) REVERT: D 187 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: D 266 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8307 (mt) REVERT: D 502 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7897 (t70) REVERT: A 22 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8728 (mt) REVERT: A 37 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8569 (mp) REVERT: A 187 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7809 (mt-10) REVERT: A 465 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7827 (ttmt) REVERT: B 22 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8729 (mt) REVERT: B 37 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8609 (mp) REVERT: B 187 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: B 465 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7867 (ttmt) REVERT: C 111 LEU cc_start: 0.4493 (OUTLIER) cc_final: 0.3838 (pp) REVERT: F 68 SER cc_start: 0.7180 (p) cc_final: 0.6594 (m) REVERT: I 107 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7617 (tttp) outliers start: 105 outliers final: 66 residues processed: 230 average time/residue: 1.1104 time to fit residues: 291.2353 Evaluate side-chains 229 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 149 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 492 CYS Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 107 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 201 ASN D 382 GLN D 404 ASN D 469 GLN A 469 GLN B 469 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17493 Z= 0.215 Angle : 0.598 8.179 23760 Z= 0.311 Chirality : 0.046 0.363 2670 Planarity : 0.005 0.046 3030 Dihedral : 7.498 59.586 3096 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.20 % Favored : 96.38 % Rotamer: Outliers : 4.99 % Allowed : 21.51 % Favored : 73.50 % 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: 0.37 (0.18), residues: 2127 helix: 2.34 (0.28), residues: 348 sheet: 1.30 (0.20), residues: 600 loop : -1.03 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.006 0.001 HIS D 25 PHE 0.016 0.002 PHE D 128 TYR 0.013 0.001 TYR H 95 ARG 0.002 0.000 ARG E 30 *********************** 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 248 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 159 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8376 (mp) REVERT: D 187 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: D 502 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7891 (t70) REVERT: A 22 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8651 (mt) REVERT: A 187 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7792 (mt-10) REVERT: A 465 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7996 (ttmt) REVERT: B 22 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8700 (mt) REVERT: B 187 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: B 465 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7732 (ttmt) REVERT: C 111 LEU cc_start: 0.4496 (OUTLIER) cc_final: 0.3853 (pp) REVERT: F 64 SER cc_start: 0.7564 (m) cc_final: 0.7187 (t) REVERT: F 68 SER cc_start: 0.7216 (p) cc_final: 0.6665 (m) REVERT: F 71 SER cc_start: 0.7692 (m) cc_final: 0.7464 (t) REVERT: I 68 SER cc_start: 0.7126 (p) cc_final: 0.6570 (m) outliers start: 89 outliers final: 59 residues processed: 224 average time/residue: 1.1179 time to fit residues: 283.9865 Evaluate side-chains 219 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 150 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 7.9990 chunk 191 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 201 ASN D 382 GLN D 404 ASN D 469 GLN A 469 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17493 Z= 0.408 Angle : 0.735 9.075 23760 Z= 0.382 Chirality : 0.052 0.447 2670 Planarity : 0.005 0.049 3030 Dihedral : 7.709 58.530 3094 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.06 % Favored : 96.43 % Rotamer: Outliers : 5.27 % Allowed : 21.46 % Favored : 73.28 % 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: 0.21 (0.17), residues: 2127 helix: 1.98 (0.28), residues: 351 sheet: 1.29 (0.20), residues: 600 loop : -1.13 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 93 HIS 0.009 0.002 HIS D 25 PHE 0.017 0.003 PHE B 128 TYR 0.018 0.002 TYR D 215 ARG 0.003 0.001 ARG D 238 *********************** 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 242 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 148 time to evaluate : 2.062 Fit side-chains revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8411 (mp) REVERT: D 187 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: D 266 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8316 (mt) REVERT: D 502 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7930 (t70) REVERT: A 22 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8748 (mt) REVERT: A 37 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8559 (mp) REVERT: A 187 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: A 465 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7925 (ttmt) REVERT: B 22 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8777 (mt) REVERT: B 187 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: B 465 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7987 (ttmt) REVERT: C 111 LEU cc_start: 0.4575 (OUTLIER) cc_final: 0.3895 (pp) REVERT: F 68 SER cc_start: 0.7234 (p) cc_final: 0.6615 (m) REVERT: I 107 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7648 (tttp) outliers start: 94 outliers final: 62 residues processed: 222 average time/residue: 1.1269 time to fit residues: 288.0727 Evaluate side-chains 221 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 146 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 492 CYS Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 107 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 4.9990 chunk 119 optimal weight: 0.0970 chunk 93 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 206 optimal weight: 0.7980 chunk 189 optimal weight: 0.6980 chunk 164 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 371 GLN A 469 GLN B 469 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17493 Z= 0.156 Angle : 0.559 7.798 23760 Z= 0.290 Chirality : 0.045 0.370 2670 Planarity : 0.004 0.044 3030 Dihedral : 7.283 59.349 3094 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.68 % Favored : 96.94 % Rotamer: Outliers : 3.53 % Allowed : 23.03 % Favored : 73.45 % 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: 0.43 (0.18), residues: 2127 helix: 2.34 (0.28), residues: 351 sheet: 1.34 (0.20), residues: 600 loop : -0.99 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS D 25 PHE 0.016 0.001 PHE A 128 TYR 0.011 0.001 TYR H 95 ARG 0.001 0.000 ARG B 325 ********************** 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 221 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 158 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 502 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7904 (t70) REVERT: A 187 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: A 465 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7892 (ttmt) REVERT: B 187 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7821 (mp0) REVERT: B 465 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7639 (ttmt) REVERT: C 68 SER cc_start: 0.7197 (p) cc_final: 0.6635 (m) REVERT: C 111 LEU cc_start: 0.4619 (OUTLIER) cc_final: 0.3970 (pp) REVERT: F 64 SER cc_start: 0.7499 (m) cc_final: 0.7124 (t) REVERT: F 68 SER cc_start: 0.7183 (p) cc_final: 0.6635 (m) REVERT: F 71 SER cc_start: 0.7693 (m) cc_final: 0.7457 (t) REVERT: I 68 SER cc_start: 0.7109 (p) cc_final: 0.6580 (m) outliers start: 63 outliers final: 43 residues processed: 200 average time/residue: 1.1977 time to fit residues: 269.0199 Evaluate side-chains 206 residues out of total 1827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 157 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 371 GLN Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.146495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110773 restraints weight = 20194.340| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.07 r_work: 0.3294 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.175 17493 Z= 0.284 Angle : 0.798 59.193 23760 Z= 0.437 Chirality : 0.049 0.959 2670 Planarity : 0.005 0.067 3030 Dihedral : 7.309 59.414 3094 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.73 % Favored : 96.94 % Rotamer: Outliers : 3.19 % Allowed : 23.47 % Favored : 73.33 % Cbeta Deviations : 0.05 % 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: 0.44 (0.18), residues: 2127 helix: 2.34 (0.28), residues: 351 sheet: 1.34 (0.20), residues: 600 loop : -0.98 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS D 25 PHE 0.015 0.002 PHE A 128 TYR 0.011 0.001 TYR H 95 ARG 0.001 0.000 ARG A 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5890.08 seconds wall clock time: 105 minutes 54.87 seconds (6354.87 seconds total)