Starting phenix.real_space_refine on Sun Mar 17 20:45:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pci_20301/03_2024/6pci_20301.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pci_20301/03_2024/6pci_20301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pci_20301/03_2024/6pci_20301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pci_20301/03_2024/6pci_20301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pci_20301/03_2024/6pci_20301.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pci_20301/03_2024/6pci_20301.pdb" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 11925 2.51 5 N 3153 2.21 5 O 3684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 72": "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: 18828 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain breaks: 1 Chain: "H" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1033 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain: "K" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Chain: "D" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 769 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "Q" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "N" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "B" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain breaks: 1 Chain: "I" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1033 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Chain: "E" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 769 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "R" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "O" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "C" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain breaks: 1 Chain: "J" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1033 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain: "M" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Chain: "F" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 769 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "S" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "P" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.60, per 1000 atoms: 0.51 Number of scatterers: 18828 At special positions: 0 Unit cell: (156.56, 148.32, 122.57, 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 66 16.00 O 3684 8.00 N 3153 7.00 C 11925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.02 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 89 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 95 " distance=2.04 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.02 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 89 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 95 " distance=2.04 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.02 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.02 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 89 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 95 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 401 " - " ASN A 257 " " NAG A 402 " - " ASN A 238 " " NAG A 403 " - " ASN A 228 " " NAG A 404 " - " ASN A 268 " " NAG B 401 " - " ASN B 257 " " NAG B 402 " - " ASN B 238 " " NAG B 403 " - " ASN B 228 " " NAG B 404 " - " ASN B 268 " " NAG C 401 " - " ASN C 257 " " NAG C 402 " - " ASN C 238 " " NAG C 403 " - " ASN C 228 " " NAG C 404 " - " ASN C 268 " " NAG G 1 " - " ASN D 563 " " NAG T 1 " - " ASN E 563 " " NAG U 1 " - " ASN F 563 " Time building additional restraints: 6.85 Conformation dependent library (CDL) restraints added in 3.2 seconds 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4314 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 51 sheets defined 13.1% alpha, 38.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'H' and resid 62 through 65 removed outlier: 4.082A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.996A pdb=" N SER K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 536 Processing helix chain 'D' and resid 538 through 541 Processing helix chain 'D' and resid 553 through 576 removed outlier: 4.665A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 Processing helix chain 'Q' and resid 80 through 84 Processing helix chain 'N' and resid 61 through 64 removed outlier: 3.594A pdb=" N LYS N 64 " --> pdb=" O PRO N 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 61 through 64' Processing helix chain 'N' and resid 86 through 90 Processing helix chain 'B' and resid 59 through 63 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'I' and resid 62 through 65 removed outlier: 4.081A pdb=" N LYS I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.996A pdb=" N SER L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 536 Processing helix chain 'E' and resid 538 through 541 Processing helix chain 'E' and resid 553 through 576 removed outlier: 4.664A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA E 575 " --> pdb=" O LEU E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 598 Processing helix chain 'R' and resid 80 through 84 Processing helix chain 'O' and resid 61 through 64 removed outlier: 3.595A pdb=" N LYS O 64 " --> pdb=" O PRO O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 86 through 90 Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'J' and resid 62 through 65 removed outlier: 4.082A pdb=" N LYS J 65 " --> pdb=" O ASP J 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 62 through 65' Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.997A pdb=" N SER M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 536 Processing helix chain 'F' and resid 538 through 541 Processing helix chain 'F' and resid 553 through 576 removed outlier: 4.665A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA F 575 " --> pdb=" O LEU F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 Processing helix chain 'S' and resid 80 through 84 Processing helix chain 'P' and resid 61 through 64 removed outlier: 3.595A pdb=" N LYS P 64 " --> pdb=" O PRO P 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 61 through 64' Processing helix chain 'P' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA2, first strand: chain 'D' and resid 543 through 548 removed outlier: 4.029A pdb=" N MET D 548 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU D 515 " --> pdb=" O MET D 548 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 165 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 114 removed outlier: 7.124A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 242 removed outlier: 7.216A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 272 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 274 " --> pdb=" O SER H 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.524A pdb=" N GLU H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.524A pdb=" N GLU H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.469A pdb=" N GLY H 10 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.469A pdb=" N GLY H 10 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N CYS H 96 " --> pdb=" O TRP H 121 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TRP H 121 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS H 98 " --> pdb=" O ASP H 119 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA H 117 " --> pdb=" O LEU H 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'K' and resid 12 through 14 removed outlier: 6.844A pdb=" N ALA K 13 " --> pdb=" O LYS K 107 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR K 87 " --> pdb=" O TYR K 36 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA K 34 " --> pdb=" O GLN K 89 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'Q' and resid 10 through 13 removed outlier: 3.617A pdb=" N ALA Q 85 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL Q 86 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE Q 34 " --> pdb=" O SER Q 50 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER Q 50 " --> pdb=" O PHE Q 34 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 10 through 13 removed outlier: 3.617A pdb=" N ALA Q 85 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'N' and resid 57 through 59 removed outlier: 6.617A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AC1, first strand: chain 'E' and resid 543 through 548 removed outlier: 4.029A pdb=" N MET E 548 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU E 515 " --> pdb=" O MET E 548 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 165 " --> pdb=" O TYR B 162 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AC3, first strand: chain 'B' and resid 107 through 114 removed outlier: 7.124A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL B 138 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 240 through 242 removed outlier: 7.216A pdb=" N TYR B 241 " --> pdb=" O TRP B 275 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS B 272 " --> pdb=" O TYR I 115 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR I 115 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B 274 " --> pdb=" O SER I 113 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER I 113 " --> pdb=" O ILE B 274 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.524A pdb=" N GLU I 5 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU I 81 " --> pdb=" O LEU I 20 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.524A pdb=" N GLU I 5 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU I 81 " --> pdb=" O LEU I 20 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.469A pdb=" N GLY I 10 " --> pdb=" O THR I 128 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET I 34 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.469A pdb=" N GLY I 10 " --> pdb=" O THR I 128 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N CYS I 96 " --> pdb=" O TRP I 121 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TRP I 121 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS I 98 " --> pdb=" O ASP I 119 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA I 117 " --> pdb=" O LEU I 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.844A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'R' and resid 10 through 13 removed outlier: 3.617A pdb=" N ALA R 85 " --> pdb=" O LEU R 105 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL R 86 " --> pdb=" O GLN R 39 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE R 34 " --> pdb=" O SER R 50 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER R 50 " --> pdb=" O PHE R 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP R 36 " --> pdb=" O LEU R 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 10 through 13 removed outlier: 3.617A pdb=" N ALA R 85 " --> pdb=" O LEU R 105 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.616A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 36 through 38 Processing sheet with id=AD9, first strand: chain 'F' and resid 543 through 548 removed outlier: 4.029A pdb=" N MET F 548 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU F 515 " --> pdb=" O MET F 548 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 165 " --> pdb=" O TYR C 162 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AE2, first strand: chain 'C' and resid 107 through 114 removed outlier: 7.125A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 240 through 242 removed outlier: 7.217A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS C 272 " --> pdb=" O TYR J 115 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 274 " --> pdb=" O SER J 113 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.525A pdb=" N GLU J 5 " --> pdb=" O ALA J 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU J 81 " --> pdb=" O LEU J 20 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.525A pdb=" N GLU J 5 " --> pdb=" O ALA J 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU J 81 " --> pdb=" O LEU J 20 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.469A pdb=" N GLY J 10 " --> pdb=" O THR J 128 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET J 34 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.469A pdb=" N GLY J 10 " --> pdb=" O THR J 128 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N CYS J 96 " --> pdb=" O TRP J 121 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TRP J 121 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS J 98 " --> pdb=" O ASP J 119 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA J 117 " --> pdb=" O LEU J 100 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'M' and resid 12 through 14 removed outlier: 6.843A pdb=" N ALA M 13 " --> pdb=" O LYS M 107 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR M 87 " --> pdb=" O TYR M 36 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA M 34 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'S' and resid 10 through 13 removed outlier: 3.616A pdb=" N ALA S 85 " --> pdb=" O LEU S 105 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL S 86 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE S 34 " --> pdb=" O SER S 50 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER S 50 " --> pdb=" O PHE S 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP S 36 " --> pdb=" O LEU S 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 10 through 13 removed outlier: 3.616A pdb=" N ALA S 85 " --> pdb=" O LEU S 105 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AF6, first strand: chain 'P' and resid 57 through 59 removed outlier: 6.616A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR P 50 " --> pdb=" O TRP P 34 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP P 34 " --> pdb=" O TYR P 50 " (cutoff:3.500A) 706 hydrogen bonds defined for protein. 1749 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: 6.34 Time building geometry restraints manager: 7.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3167 1.32 - 1.45: 5691 1.45 - 1.57: 10321 1.57 - 1.70: 0 1.70 - 1.83: 87 Bond restraints: 19266 Sorted by residual: bond pdb=" C ALA E 507 " pdb=" N GLN E 508 " ideal model delta sigma weight residual 1.329 1.234 0.095 3.03e-02 1.09e+03 9.81e+00 bond pdb=" C ALA F 507 " pdb=" N GLN F 508 " ideal model delta sigma weight residual 1.329 1.234 0.095 3.03e-02 1.09e+03 9.78e+00 bond pdb=" C ALA D 507 " pdb=" N GLN D 508 " ideal model delta sigma weight residual 1.329 1.234 0.094 3.03e-02 1.09e+03 9.71e+00 bond pdb=" N PHE F 517 " pdb=" CA PHE F 517 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.29e-02 6.01e+03 6.39e+00 bond pdb=" N PHE D 517 " pdb=" CA PHE D 517 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.29e-02 6.01e+03 6.20e+00 ... (remaining 19261 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.22: 459 106.22 - 113.19: 10555 113.19 - 120.16: 6555 120.16 - 127.13: 8354 127.13 - 134.10: 249 Bond angle restraints: 26172 Sorted by residual: angle pdb=" C GLY Q 51 " pdb=" N THR Q 52 " pdb=" CA THR Q 52 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C GLY R 51 " pdb=" N THR R 52 " pdb=" CA THR R 52 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C GLY S 51 " pdb=" N THR S 52 " pdb=" CA THR S 52 " ideal model delta sigma weight residual 121.54 129.17 -7.63 1.91e+00 2.74e-01 1.60e+01 angle pdb=" N ASN B 257 " pdb=" CA ASN B 257 " pdb=" CB ASN B 257 " ideal model delta sigma weight residual 110.28 116.38 -6.10 1.55e+00 4.16e-01 1.55e+01 angle pdb=" N ASN C 257 " pdb=" CA ASN C 257 " pdb=" CB ASN C 257 " ideal model delta sigma weight residual 110.28 116.36 -6.08 1.55e+00 4.16e-01 1.54e+01 ... (remaining 26167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.77: 11308 20.77 - 41.54: 266 41.54 - 62.31: 51 62.31 - 83.09: 18 83.09 - 103.86: 12 Dihedral angle restraints: 11655 sinusoidal: 4860 harmonic: 6795 Sorted by residual: dihedral pdb=" CA SER M 30 " pdb=" C SER M 30 " pdb=" N ASN M 31 " pdb=" CA ASN M 31 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA SER K 30 " pdb=" C SER K 30 " pdb=" N ASN K 31 " pdb=" CA ASN K 31 " ideal model delta harmonic sigma weight residual 180.00 150.04 29.96 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA SER L 30 " pdb=" C SER L 30 " pdb=" N ASN L 31 " pdb=" CA ASN L 31 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 11652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2703 0.103 - 0.206: 231 0.206 - 0.309: 9 0.309 - 0.412: 6 0.412 - 0.515: 3 Chirality restraints: 2952 Sorted by residual: chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 268 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.64e+00 chirality pdb=" C1 NAG A 404 " pdb=" ND2 ASN A 268 " pdb=" C2 NAG A 404 " pdb=" O5 NAG A 404 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" C1 NAG B 404 " pdb=" ND2 ASN B 268 " pdb=" C2 NAG B 404 " pdb=" O5 NAG B 404 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.57e+00 ... (remaining 2949 not shown) Planarity restraints: 3330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 257 " -0.006 2.00e-02 2.50e+03 2.35e-02 6.92e+00 pdb=" CG ASN B 257 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN B 257 " -0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN B 257 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG B 401 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 92 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.84e+00 pdb=" C LYS K 92 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS K 92 " -0.017 2.00e-02 2.50e+03 pdb=" N SER K 93 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 257 " -0.006 2.00e-02 2.50e+03 2.34e-02 6.84e+00 pdb=" CG ASN C 257 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN C 257 " -0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN C 257 " 0.018 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " -0.020 2.00e-02 2.50e+03 ... (remaining 3327 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4982 2.79 - 3.32: 15956 3.32 - 3.85: 32024 3.85 - 4.37: 36136 4.37 - 4.90: 61036 Nonbonded interactions: 150134 Sorted by model distance: nonbonded pdb=" O GLY A 224 " pdb=" OG1 THR A 230 " model vdw 2.268 2.440 nonbonded pdb=" O GLY B 224 " pdb=" OG1 THR B 230 " model vdw 2.269 2.440 nonbonded pdb=" O GLY C 224 " pdb=" OG1 THR C 230 " model vdw 2.269 2.440 nonbonded pdb=" NE2 GLN L 90 " pdb=" O SER L 93 " model vdw 2.274 2.520 nonbonded pdb=" NE2 GLN M 90 " pdb=" O SER M 93 " model vdw 2.277 2.520 ... (remaining 150129 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 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.920 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 48.270 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 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 : 0.009 0.095 19266 Z= 0.615 Angle : 1.052 10.317 26172 Z= 0.578 Chirality : 0.061 0.515 2952 Planarity : 0.007 0.050 3315 Dihedral : 10.797 103.857 7278 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -2.72 (0.16), residues: 2340 helix: -2.31 (0.30), residues: 201 sheet: -1.81 (0.16), residues: 933 loop : -1.61 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP A 104 HIS 0.009 0.003 HIS E 516 PHE 0.025 0.004 PHE D 582 TYR 0.028 0.004 TYR A 109 ARG 0.006 0.001 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 774 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8991 (mt0) cc_final: 0.8716 (mt0) REVERT: A 106 GLU cc_start: 0.8713 (tp30) cc_final: 0.7930 (tp30) REVERT: A 117 ASP cc_start: 0.8719 (p0) cc_final: 0.8377 (p0) REVERT: A 261 TYR cc_start: 0.7926 (m-10) cc_final: 0.7716 (m-10) REVERT: H 12 VAL cc_start: 0.6934 (t) cc_final: 0.6240 (t) REVERT: H 18 LEU cc_start: 0.8153 (tp) cc_final: 0.7752 (tt) REVERT: H 20 LEU cc_start: 0.8295 (mt) cc_final: 0.8071 (mp) REVERT: H 45 LEU cc_start: 0.7673 (tp) cc_final: 0.7317 (tp) REVERT: H 57 LYS cc_start: 0.8460 (tppt) cc_final: 0.8245 (tttm) REVERT: H 80 TYR cc_start: 0.8596 (m-10) cc_final: 0.8328 (m-80) REVERT: K 36 TYR cc_start: 0.8091 (m-10) cc_final: 0.7886 (m-80) REVERT: K 47 LEU cc_start: 0.9329 (mt) cc_final: 0.8917 (mt) REVERT: K 78 LEU cc_start: 0.7286 (mt) cc_final: 0.6777 (mt) REVERT: K 79 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8233 (tp40) REVERT: K 89 GLN cc_start: 0.8367 (tt0) cc_final: 0.7888 (tt0) REVERT: K 92 LYS cc_start: 0.8837 (tttt) cc_final: 0.8465 (tppt) REVERT: K 104 LEU cc_start: 0.7012 (tp) cc_final: 0.5624 (tp) REVERT: D 532 ILE cc_start: 0.9441 (mt) cc_final: 0.9156 (pt) REVERT: D 597 TRP cc_start: 0.7619 (t-100) cc_final: 0.7274 (t-100) REVERT: Q 20 THR cc_start: 0.8415 (p) cc_final: 0.7604 (p) REVERT: Q 38 GLN cc_start: 0.8945 (tt0) cc_final: 0.8672 (tt0) REVERT: Q 43 GLN cc_start: 0.8580 (mm-40) cc_final: 0.7908 (mm-40) REVERT: Q 54 THR cc_start: 0.9421 (m) cc_final: 0.9093 (p) REVERT: Q 79 LEU cc_start: 0.8430 (mt) cc_final: 0.7670 (mt) REVERT: N 77 GLN cc_start: 0.8462 (mt0) cc_final: 0.8161 (mt0) REVERT: N 100 TRP cc_start: 0.9136 (t-100) cc_final: 0.8788 (t-100) REVERT: B 62 GLN cc_start: 0.8966 (mt0) cc_final: 0.8711 (mt0) REVERT: B 106 GLU cc_start: 0.8685 (tp30) cc_final: 0.8076 (tp30) REVERT: B 117 ASP cc_start: 0.8801 (p0) cc_final: 0.8407 (p0) REVERT: B 178 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8725 (mt-10) REVERT: B 272 LYS cc_start: 0.6171 (pttt) cc_final: 0.5932 (pttm) REVERT: I 34 MET cc_start: 0.7829 (mmm) cc_final: 0.7543 (mmp) REVERT: I 45 LEU cc_start: 0.7841 (tp) cc_final: 0.7374 (tp) REVERT: I 57 LYS cc_start: 0.8529 (tppt) cc_final: 0.8310 (tttm) REVERT: I 64 VAL cc_start: 0.9132 (m) cc_final: 0.8622 (m) REVERT: I 80 TYR cc_start: 0.8695 (m-10) cc_final: 0.8445 (m-80) REVERT: I 94 TYR cc_start: 0.7281 (m-10) cc_final: 0.6769 (m-10) REVERT: I 112 HIS cc_start: 0.6153 (t-90) cc_final: 0.5632 (t-90) REVERT: L 36 TYR cc_start: 0.8168 (m-10) cc_final: 0.7950 (m-80) REVERT: L 73 LEU cc_start: 0.8171 (tp) cc_final: 0.7892 (tp) REVERT: L 89 GLN cc_start: 0.8353 (tt0) cc_final: 0.8128 (tt0) REVERT: L 92 LYS cc_start: 0.8862 (tttt) cc_final: 0.8329 (tppt) REVERT: E 532 ILE cc_start: 0.9454 (mt) cc_final: 0.9114 (pt) REVERT: E 555 ILE cc_start: 0.9017 (mt) cc_final: 0.8759 (mp) REVERT: E 597 TRP cc_start: 0.7706 (t-100) cc_final: 0.7349 (t-100) REVERT: R 13 LEU cc_start: 0.8493 (mp) cc_final: 0.8280 (mp) REVERT: R 34 PHE cc_start: 0.8449 (m-10) cc_final: 0.7830 (m-10) REVERT: R 61 ASP cc_start: 0.8457 (p0) cc_final: 0.8080 (t0) REVERT: O 35 ASN cc_start: 0.8771 (m-40) cc_final: 0.8433 (m-40) REVERT: O 58 ASN cc_start: 0.8739 (t0) cc_final: 0.8522 (t0) REVERT: O 100 TRP cc_start: 0.9169 (t-100) cc_final: 0.8497 (t-100) REVERT: C 62 GLN cc_start: 0.8834 (mt0) cc_final: 0.8569 (mt0) REVERT: C 78 ASP cc_start: 0.8116 (t0) cc_final: 0.7894 (t0) REVERT: C 106 GLU cc_start: 0.8658 (tp30) cc_final: 0.7901 (tp30) REVERT: C 117 ASP cc_start: 0.8791 (p0) cc_final: 0.8393 (p0) REVERT: C 163 ASP cc_start: 0.9356 (t0) cc_final: 0.9095 (t0) REVERT: J 12 VAL cc_start: 0.6382 (t) cc_final: 0.6085 (t) REVERT: J 36 TRP cc_start: 0.6993 (m100) cc_final: 0.5916 (m100) REVERT: J 46 GLU cc_start: 0.8743 (pt0) cc_final: 0.8224 (pm20) REVERT: J 55 ASP cc_start: 0.7712 (t70) cc_final: 0.7510 (t70) REVERT: J 57 LYS cc_start: 0.8649 (tppt) cc_final: 0.8234 (tttm) REVERT: J 64 VAL cc_start: 0.9160 (m) cc_final: 0.8698 (m) REVERT: J 80 TYR cc_start: 0.8689 (m-10) cc_final: 0.8337 (m-80) REVERT: J 83 MET cc_start: 0.8598 (mtt) cc_final: 0.8394 (mmm) REVERT: J 102 GLN cc_start: 0.8058 (mt0) cc_final: 0.7552 (mt0) REVERT: M 31 ASN cc_start: 0.7171 (p0) cc_final: 0.6784 (m-40) REVERT: M 37 GLN cc_start: 0.7919 (tt0) cc_final: 0.7699 (tt0) REVERT: M 58 VAL cc_start: 0.7347 (t) cc_final: 0.7054 (p) REVERT: M 73 LEU cc_start: 0.7992 (tp) cc_final: 0.7622 (tp) REVERT: M 85 THR cc_start: 0.6511 (m) cc_final: 0.6308 (p) REVERT: M 86 TYR cc_start: 0.6745 (m-10) cc_final: 0.6213 (m-80) REVERT: M 92 LYS cc_start: 0.8977 (tttt) cc_final: 0.8519 (ttmm) REVERT: F 581 THR cc_start: 0.9623 (m) cc_final: 0.9032 (p) REVERT: S 20 THR cc_start: 0.8465 (p) cc_final: 0.7757 (p) REVERT: S 21 LEU cc_start: 0.8399 (tp) cc_final: 0.8156 (tp) REVERT: S 34 PHE cc_start: 0.7778 (m-10) cc_final: 0.7389 (m-10) REVERT: S 47 LEU cc_start: 0.9025 (tp) cc_final: 0.8803 (tt) REVERT: S 61 ASP cc_start: 0.8279 (p0) cc_final: 0.7803 (t0) REVERT: S 84 PHE cc_start: 0.7584 (t80) cc_final: 0.7120 (t80) REVERT: S 97 TYR cc_start: 0.8644 (m-80) cc_final: 0.8427 (m-80) REVERT: P 60 ASN cc_start: 0.9117 (t0) cc_final: 0.8651 (t0) REVERT: P 100 TRP cc_start: 0.9135 (t-100) cc_final: 0.8699 (t-100) REVERT: P 112 ASP cc_start: 0.8943 (p0) cc_final: 0.8263 (p0) outliers start: 0 outliers final: 0 residues processed: 774 average time/residue: 0.3562 time to fit residues: 390.5013 Evaluate side-chains 475 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 475 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 7.9990 chunk 172 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 255 GLN H 3 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 255 GLN I 102 GLN ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 GLN C 188 GLN C 255 GLN ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 GLN ** S 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19266 Z= 0.207 Angle : 0.675 9.419 26172 Z= 0.354 Chirality : 0.049 0.371 2952 Planarity : 0.005 0.046 3315 Dihedral : 9.626 75.844 3141 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.16), residues: 2340 helix: -0.23 (0.36), residues: 165 sheet: -1.21 (0.16), residues: 870 loop : -1.14 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 104 HIS 0.005 0.001 HIS H 35 PHE 0.031 0.002 PHE I 68 TYR 0.031 0.002 TYR M 96 ARG 0.009 0.001 ARG M 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 697 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8177 (t70) cc_final: 0.7917 (t70) REVERT: A 117 ASP cc_start: 0.8610 (p0) cc_final: 0.8352 (p0) REVERT: A 150 ASP cc_start: 0.8687 (m-30) cc_final: 0.8462 (m-30) REVERT: A 272 LYS cc_start: 0.5696 (pttt) cc_final: 0.5411 (ttmm) REVERT: H 12 VAL cc_start: 0.6919 (t) cc_final: 0.6313 (t) REVERT: H 36 TRP cc_start: 0.7091 (m100) cc_final: 0.6306 (m100) REVERT: H 45 LEU cc_start: 0.7531 (tp) cc_final: 0.7315 (tp) REVERT: H 86 LEU cc_start: 0.9196 (mt) cc_final: 0.8651 (mt) REVERT: K 46 LEU cc_start: 0.8963 (pt) cc_final: 0.8727 (pt) REVERT: K 78 LEU cc_start: 0.7616 (mt) cc_final: 0.7348 (mt) REVERT: K 92 LYS cc_start: 0.8756 (tttt) cc_final: 0.8547 (tppt) REVERT: D 532 ILE cc_start: 0.9278 (mt) cc_final: 0.9039 (pt) REVERT: D 560 GLN cc_start: 0.9122 (tp40) cc_final: 0.8115 (tp40) REVERT: D 581 THR cc_start: 0.9642 (m) cc_final: 0.9384 (p) REVERT: D 592 PHE cc_start: 0.8412 (t80) cc_final: 0.7973 (t80) REVERT: Q 4 LEU cc_start: 0.8699 (mt) cc_final: 0.8493 (mt) REVERT: Q 21 LEU cc_start: 0.8297 (tp) cc_final: 0.8014 (tp) REVERT: Q 79 LEU cc_start: 0.8175 (mt) cc_final: 0.7803 (mt) REVERT: N 15 SER cc_start: 0.8911 (m) cc_final: 0.8277 (p) REVERT: N 100 TRP cc_start: 0.9106 (t-100) cc_final: 0.8663 (t-100) REVERT: B 62 GLN cc_start: 0.9189 (mt0) cc_final: 0.8542 (mt0) REVERT: B 103 GLU cc_start: 0.8256 (tt0) cc_final: 0.7895 (tt0) REVERT: B 117 ASP cc_start: 0.8695 (p0) cc_final: 0.8211 (p0) REVERT: I 34 MET cc_start: 0.7641 (mmm) cc_final: 0.7283 (mmp) REVERT: L 31 ASN cc_start: 0.7004 (p0) cc_final: 0.6391 (m-40) REVERT: L 73 LEU cc_start: 0.8315 (tp) cc_final: 0.8034 (tp) REVERT: L 89 GLN cc_start: 0.8177 (tt0) cc_final: 0.7891 (tt0) REVERT: L 90 GLN cc_start: 0.7709 (tp40) cc_final: 0.6990 (tp40) REVERT: L 92 LYS cc_start: 0.8752 (tttt) cc_final: 0.8549 (tppt) REVERT: E 529 LEU cc_start: 0.8916 (mt) cc_final: 0.8715 (mp) REVERT: E 532 ILE cc_start: 0.9273 (mt) cc_final: 0.8997 (pt) REVERT: E 534 TYR cc_start: 0.9269 (t80) cc_final: 0.8980 (t80) REVERT: E 573 LEU cc_start: 0.9616 (mt) cc_final: 0.9359 (mt) REVERT: E 579 LEU cc_start: 0.9161 (mt) cc_final: 0.8872 (tt) REVERT: E 581 THR cc_start: 0.9669 (m) cc_final: 0.9333 (p) REVERT: E 591 ASP cc_start: 0.9033 (t0) cc_final: 0.8823 (t0) REVERT: E 597 TRP cc_start: 0.7588 (t-100) cc_final: 0.7367 (t-100) REVERT: R 18 ARG cc_start: 0.8131 (ttp80) cc_final: 0.7833 (ttp80) REVERT: R 21 LEU cc_start: 0.8052 (tt) cc_final: 0.7591 (mm) REVERT: R 36 TRP cc_start: 0.8522 (m100) cc_final: 0.8259 (m100) REVERT: R 61 ASP cc_start: 0.8411 (p0) cc_final: 0.8013 (t0) REVERT: O 20 LEU cc_start: 0.9219 (mp) cc_final: 0.9012 (mm) REVERT: O 58 ASN cc_start: 0.8704 (t0) cc_final: 0.8231 (t0) REVERT: O 100 TRP cc_start: 0.9153 (t-100) cc_final: 0.8648 (t-100) REVERT: C 57 LEU cc_start: 0.9222 (tp) cc_final: 0.8832 (mp) REVERT: C 62 GLN cc_start: 0.9072 (mt0) cc_final: 0.8629 (mt0) REVERT: C 117 ASP cc_start: 0.8610 (p0) cc_final: 0.8371 (p0) REVERT: C 273 LEU cc_start: 0.7588 (mp) cc_final: 0.7243 (mp) REVERT: J 12 VAL cc_start: 0.6267 (t) cc_final: 0.6000 (t) REVERT: J 36 TRP cc_start: 0.6903 (m100) cc_final: 0.5944 (m100) REVERT: J 46 GLU cc_start: 0.8781 (pt0) cc_final: 0.8321 (pm20) REVERT: J 55 ASP cc_start: 0.7826 (t70) cc_final: 0.7570 (t70) REVERT: J 57 LYS cc_start: 0.8860 (tppt) cc_final: 0.8438 (tttm) REVERT: J 83 MET cc_start: 0.8774 (mtt) cc_final: 0.8433 (mmm) REVERT: J 86 LEU cc_start: 0.9126 (mt) cc_final: 0.8783 (mt) REVERT: J 102 GLN cc_start: 0.8148 (mt0) cc_final: 0.7750 (mt0) REVERT: M 31 ASN cc_start: 0.7157 (p0) cc_final: 0.6875 (m-40) REVERT: M 46 LEU cc_start: 0.9080 (pt) cc_final: 0.8866 (pt) REVERT: M 58 VAL cc_start: 0.7245 (t) cc_final: 0.6993 (p) REVERT: M 73 LEU cc_start: 0.8186 (tp) cc_final: 0.7708 (tp) REVERT: M 86 TYR cc_start: 0.6431 (m-10) cc_final: 0.6021 (m-80) REVERT: M 90 GLN cc_start: 0.7663 (tp40) cc_final: 0.7368 (tp40) REVERT: M 92 LYS cc_start: 0.8851 (tttt) cc_final: 0.8634 (tppt) REVERT: M 104 LEU cc_start: 0.7669 (tp) cc_final: 0.6524 (tp) REVERT: F 581 THR cc_start: 0.9670 (m) cc_final: 0.9346 (p) REVERT: S 4 LEU cc_start: 0.8699 (mt) cc_final: 0.8304 (mt) REVERT: S 61 ASP cc_start: 0.8276 (p0) cc_final: 0.7760 (t0) REVERT: S 62 ARG cc_start: 0.8374 (ptt-90) cc_final: 0.7673 (ptp90) REVERT: S 78 ARG cc_start: 0.8674 (ttp-170) cc_final: 0.8004 (ttp-170) REVERT: P 15 SER cc_start: 0.8861 (m) cc_final: 0.8520 (p) REVERT: P 32 TYR cc_start: 0.8769 (m-10) cc_final: 0.8188 (m-10) REVERT: P 60 ASN cc_start: 0.9231 (t0) cc_final: 0.8718 (t0) REVERT: P 100 TRP cc_start: 0.9084 (t-100) cc_final: 0.8658 (t-100) outliers start: 0 outliers final: 0 residues processed: 697 average time/residue: 0.3176 time to fit residues: 328.5112 Evaluate side-chains 501 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 501 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 140 optimal weight: 0.0870 chunk 57 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 224 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 166 optimal weight: 0.7980 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN B 255 GLN I 3 GLN ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19266 Z= 0.236 Angle : 0.651 10.551 26172 Z= 0.337 Chirality : 0.048 0.351 2952 Planarity : 0.004 0.072 3315 Dihedral : 8.862 68.027 3141 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2340 helix: 0.02 (0.36), residues: 201 sheet: -0.94 (0.17), residues: 867 loop : -0.95 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 104 HIS 0.003 0.001 HIS H 35 PHE 0.031 0.002 PHE Q 72 TYR 0.035 0.002 TYR H 114 ARG 0.011 0.001 ARG J 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 615 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8184 (t70) cc_final: 0.7914 (t70) REVERT: A 117 ASP cc_start: 0.8565 (p0) cc_final: 0.8306 (p0) REVERT: H 36 TRP cc_start: 0.7133 (m100) cc_final: 0.6220 (m100) REVERT: H 57 LYS cc_start: 0.8871 (tptt) cc_final: 0.8303 (tttm) REVERT: H 86 LEU cc_start: 0.9000 (mt) cc_final: 0.8720 (mt) REVERT: H 102 GLN cc_start: 0.8251 (mt0) cc_final: 0.7545 (mt0) REVERT: H 114 TYR cc_start: 0.6533 (m-10) cc_final: 0.5996 (m-10) REVERT: K 46 LEU cc_start: 0.9020 (pt) cc_final: 0.8755 (pt) REVERT: K 92 LYS cc_start: 0.8748 (tttt) cc_final: 0.8540 (tppt) REVERT: D 532 ILE cc_start: 0.9289 (mt) cc_final: 0.9060 (pt) REVERT: D 564 GLU cc_start: 0.7902 (mp0) cc_final: 0.7696 (mp0) REVERT: D 581 THR cc_start: 0.9673 (m) cc_final: 0.9355 (p) REVERT: D 592 PHE cc_start: 0.8401 (t80) cc_final: 0.7988 (t80) REVERT: Q 4 LEU cc_start: 0.8639 (mt) cc_final: 0.8392 (mt) REVERT: N 15 SER cc_start: 0.8903 (m) cc_final: 0.8213 (p) REVERT: N 52 HIS cc_start: 0.7656 (t-90) cc_final: 0.6927 (t-90) REVERT: B 62 GLN cc_start: 0.9107 (mt0) cc_final: 0.8399 (mt0) REVERT: B 117 ASP cc_start: 0.8747 (p0) cc_final: 0.8283 (p0) REVERT: I 34 MET cc_start: 0.7738 (mmm) cc_final: 0.7278 (mmp) REVERT: I 48 MET cc_start: 0.8307 (mmm) cc_final: 0.7912 (tpp) REVERT: I 76 LYS cc_start: 0.8770 (mtmm) cc_final: 0.8431 (ptpp) REVERT: I 80 TYR cc_start: 0.8436 (m-80) cc_final: 0.8222 (m-10) REVERT: L 31 ASN cc_start: 0.6969 (p0) cc_final: 0.6515 (m-40) REVERT: L 70 ASP cc_start: 0.7434 (t0) cc_final: 0.6885 (p0) REVERT: L 73 LEU cc_start: 0.8409 (tp) cc_final: 0.8055 (tp) REVERT: L 92 LYS cc_start: 0.8640 (tttt) cc_final: 0.8333 (tppt) REVERT: E 529 LEU cc_start: 0.8998 (mt) cc_final: 0.8720 (mp) REVERT: E 532 ILE cc_start: 0.9270 (mt) cc_final: 0.9003 (pt) REVERT: E 547 LEU cc_start: 0.9187 (mp) cc_final: 0.8965 (mp) REVERT: E 565 THR cc_start: 0.9146 (p) cc_final: 0.8770 (t) REVERT: E 573 LEU cc_start: 0.9626 (mt) cc_final: 0.9353 (mm) REVERT: E 579 LEU cc_start: 0.9204 (mt) cc_final: 0.8888 (tt) REVERT: E 581 THR cc_start: 0.9683 (m) cc_final: 0.9409 (p) REVERT: E 591 ASP cc_start: 0.9089 (t0) cc_final: 0.8835 (t0) REVERT: E 597 TRP cc_start: 0.7732 (t-100) cc_final: 0.7429 (t-100) REVERT: R 18 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7802 (ttp80) REVERT: R 61 ASP cc_start: 0.8439 (p0) cc_final: 0.7941 (t0) REVERT: O 58 ASN cc_start: 0.8744 (t0) cc_final: 0.8260 (t0) REVERT: C 39 HIS cc_start: 0.8174 (t70) cc_final: 0.7963 (t70) REVERT: C 57 LEU cc_start: 0.9088 (tp) cc_final: 0.8738 (mp) REVERT: C 62 GLN cc_start: 0.8952 (mt0) cc_final: 0.8507 (mt0) REVERT: C 273 LEU cc_start: 0.7507 (mp) cc_final: 0.7163 (mp) REVERT: J 12 VAL cc_start: 0.6224 (t) cc_final: 0.5904 (t) REVERT: J 46 GLU cc_start: 0.8696 (pt0) cc_final: 0.8298 (pm20) REVERT: J 55 ASP cc_start: 0.7910 (t70) cc_final: 0.7619 (t70) REVERT: J 57 LYS cc_start: 0.8947 (tppt) cc_final: 0.8587 (tttm) REVERT: J 80 TYR cc_start: 0.8309 (m-80) cc_final: 0.8108 (m-80) REVERT: J 83 MET cc_start: 0.8679 (mtt) cc_final: 0.8298 (mmm) REVERT: J 86 LEU cc_start: 0.9124 (mt) cc_final: 0.8885 (mt) REVERT: J 102 GLN cc_start: 0.8167 (mt0) cc_final: 0.7703 (mt0) REVERT: J 128 THR cc_start: 0.9226 (p) cc_final: 0.8968 (t) REVERT: M 58 VAL cc_start: 0.7372 (t) cc_final: 0.7076 (p) REVERT: M 73 LEU cc_start: 0.8059 (tp) cc_final: 0.7591 (tp) REVERT: M 79 GLN cc_start: 0.5999 (pt0) cc_final: 0.5200 (pp30) REVERT: M 90 GLN cc_start: 0.7839 (tp-100) cc_final: 0.7369 (tp40) REVERT: F 581 THR cc_start: 0.9686 (m) cc_final: 0.9384 (p) REVERT: F 592 PHE cc_start: 0.8215 (t80) cc_final: 0.7825 (t80) REVERT: S 4 LEU cc_start: 0.8511 (mt) cc_final: 0.8274 (mt) REVERT: S 18 ARG cc_start: 0.8657 (ttp80) cc_final: 0.8275 (ttp80) REVERT: S 20 THR cc_start: 0.8519 (p) cc_final: 0.8020 (p) REVERT: S 79 LEU cc_start: 0.8184 (mt) cc_final: 0.7910 (mt) REVERT: S 96 LEU cc_start: 0.9439 (mp) cc_final: 0.9204 (mm) REVERT: P 15 SER cc_start: 0.8876 (m) cc_final: 0.8426 (p) REVERT: P 52 HIS cc_start: 0.7653 (t-90) cc_final: 0.7075 (t-90) REVERT: P 60 ASN cc_start: 0.9275 (t0) cc_final: 0.8767 (t0) outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 0.3040 time to fit residues: 280.2746 Evaluate side-chains 488 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 488 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 139 optimal weight: 0.5980 chunk 208 optimal weight: 0.5980 chunk 220 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 197 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 GLN B 255 GLN I 31 ASN ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN M 79 GLN ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19266 Z= 0.189 Angle : 0.627 7.510 26172 Z= 0.321 Chirality : 0.048 0.334 2952 Planarity : 0.004 0.045 3315 Dihedral : 8.031 58.654 3141 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.17), residues: 2340 helix: 0.90 (0.39), residues: 183 sheet: -0.74 (0.17), residues: 888 loop : -0.87 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 114 HIS 0.005 0.001 HIS J 35 PHE 0.029 0.002 PHE Q 34 TYR 0.015 0.002 TYR L 96 ARG 0.010 0.000 ARG H 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 621 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.8333 (t70) cc_final: 0.8079 (t70) REVERT: A 57 LEU cc_start: 0.9138 (tp) cc_final: 0.8783 (mp) REVERT: A 78 ASP cc_start: 0.8155 (t70) cc_final: 0.7928 (t70) REVERT: A 117 ASP cc_start: 0.8657 (p0) cc_final: 0.8348 (p0) REVERT: H 36 TRP cc_start: 0.6943 (m100) cc_final: 0.6132 (m100) REVERT: H 114 TYR cc_start: 0.6520 (m-10) cc_final: 0.5802 (m-10) REVERT: K 46 LEU cc_start: 0.9016 (pt) cc_final: 0.8718 (pt) REVERT: K 89 GLN cc_start: 0.8215 (tt0) cc_final: 0.7898 (tt0) REVERT: K 94 PHE cc_start: 0.9115 (m-80) cc_final: 0.8744 (m-10) REVERT: K 104 LEU cc_start: 0.7371 (tp) cc_final: 0.6711 (tp) REVERT: D 512 ASN cc_start: 0.9074 (t0) cc_final: 0.8842 (t0) REVERT: D 532 ILE cc_start: 0.9177 (mt) cc_final: 0.8915 (pt) REVERT: D 560 GLN cc_start: 0.8504 (tp40) cc_final: 0.8103 (tp40) REVERT: D 579 LEU cc_start: 0.9141 (mm) cc_final: 0.8858 (tt) REVERT: Q 79 LEU cc_start: 0.8338 (mt) cc_final: 0.7995 (mt) REVERT: N 15 SER cc_start: 0.8934 (m) cc_final: 0.8164 (p) REVERT: N 52 HIS cc_start: 0.7489 (t-90) cc_final: 0.6612 (t-90) REVERT: B 62 GLN cc_start: 0.8953 (mt0) cc_final: 0.8441 (mt0) REVERT: B 117 ASP cc_start: 0.8686 (p0) cc_final: 0.8282 (p0) REVERT: I 34 MET cc_start: 0.7762 (mmm) cc_final: 0.7216 (mmp) REVERT: I 48 MET cc_start: 0.8209 (mmm) cc_final: 0.7977 (tpp) REVERT: I 59 PHE cc_start: 0.7054 (t80) cc_final: 0.6791 (t80) REVERT: I 76 LYS cc_start: 0.8782 (mtmm) cc_final: 0.8435 (ptpp) REVERT: I 80 TYR cc_start: 0.8213 (m-80) cc_final: 0.7320 (m-80) REVERT: L 24 ARG cc_start: 0.7351 (mmm-85) cc_final: 0.6881 (mmm-85) REVERT: L 70 ASP cc_start: 0.7339 (t0) cc_final: 0.6761 (p0) REVERT: L 73 LEU cc_start: 0.8374 (tp) cc_final: 0.7981 (tp) REVERT: L 75 ILE cc_start: 0.5837 (mt) cc_final: 0.5619 (mt) REVERT: L 92 LYS cc_start: 0.8658 (tttt) cc_final: 0.8276 (tppt) REVERT: L 93 SER cc_start: 0.8562 (p) cc_final: 0.8344 (t) REVERT: L 104 LEU cc_start: 0.7752 (tp) cc_final: 0.7310 (tt) REVERT: E 565 THR cc_start: 0.9157 (p) cc_final: 0.8785 (t) REVERT: E 573 LEU cc_start: 0.9600 (mt) cc_final: 0.9367 (mm) REVERT: E 579 LEU cc_start: 0.9171 (mt) cc_final: 0.8901 (tt) REVERT: E 581 THR cc_start: 0.9677 (m) cc_final: 0.9424 (p) REVERT: E 591 ASP cc_start: 0.9107 (t0) cc_final: 0.8798 (t0) REVERT: E 597 TRP cc_start: 0.7569 (t-100) cc_final: 0.7320 (t-100) REVERT: R 61 ASP cc_start: 0.8440 (p0) cc_final: 0.7913 (t0) REVERT: R 76 ILE cc_start: 0.9274 (mp) cc_final: 0.8933 (tt) REVERT: R 96 LEU cc_start: 0.9469 (mp) cc_final: 0.9157 (tt) REVERT: R 106 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7412 (tm-30) REVERT: O 58 ASN cc_start: 0.8731 (t0) cc_final: 0.8405 (t0) REVERT: C 57 LEU cc_start: 0.8999 (tp) cc_final: 0.8735 (mp) REVERT: C 62 GLN cc_start: 0.9011 (mt0) cc_final: 0.8594 (mt0) REVERT: C 68 LEU cc_start: 0.9396 (mt) cc_final: 0.9111 (mt) REVERT: C 273 LEU cc_start: 0.7442 (mp) cc_final: 0.7137 (mp) REVERT: J 12 VAL cc_start: 0.6190 (t) cc_final: 0.5974 (t) REVERT: J 46 GLU cc_start: 0.8769 (pt0) cc_final: 0.8331 (pm20) REVERT: J 55 ASP cc_start: 0.7914 (t70) cc_final: 0.7597 (t70) REVERT: J 68 PHE cc_start: 0.7889 (m-80) cc_final: 0.7672 (m-10) REVERT: J 79 LEU cc_start: 0.8173 (tt) cc_final: 0.7945 (tt) REVERT: J 80 TYR cc_start: 0.8320 (m-80) cc_final: 0.8030 (m-80) REVERT: J 82 GLN cc_start: 0.8101 (tp40) cc_final: 0.7674 (tp-100) REVERT: J 83 MET cc_start: 0.8728 (mtt) cc_final: 0.8452 (mmm) REVERT: J 86 LEU cc_start: 0.9145 (mt) cc_final: 0.8849 (mt) REVERT: J 102 GLN cc_start: 0.8111 (mt0) cc_final: 0.7636 (mt0) REVERT: M 58 VAL cc_start: 0.7452 (t) cc_final: 0.7028 (p) REVERT: M 73 LEU cc_start: 0.7983 (tp) cc_final: 0.7503 (tp) REVERT: M 79 GLN cc_start: 0.6040 (pt0) cc_final: 0.5318 (pp30) REVERT: M 90 GLN cc_start: 0.7866 (tp-100) cc_final: 0.7217 (tp40) REVERT: F 581 THR cc_start: 0.9687 (m) cc_final: 0.9436 (p) REVERT: F 592 PHE cc_start: 0.8176 (t80) cc_final: 0.7786 (t80) REVERT: S 4 LEU cc_start: 0.8450 (mt) cc_final: 0.8226 (mt) REVERT: S 18 ARG cc_start: 0.8696 (ttp80) cc_final: 0.8299 (ttp80) REVERT: S 20 THR cc_start: 0.8510 (p) cc_final: 0.8027 (p) REVERT: S 79 LEU cc_start: 0.8174 (mt) cc_final: 0.7884 (mt) REVERT: S 96 LEU cc_start: 0.9471 (mp) cc_final: 0.9159 (tt) REVERT: P 15 SER cc_start: 0.8953 (m) cc_final: 0.8531 (p) REVERT: P 52 HIS cc_start: 0.7502 (t-90) cc_final: 0.7021 (t-90) REVERT: P 60 ASN cc_start: 0.9288 (t0) cc_final: 0.8750 (t0) outliers start: 1 outliers final: 0 residues processed: 622 average time/residue: 0.2986 time to fit residues: 281.4830 Evaluate side-chains 479 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 479 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 197 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN I 31 ASN I 82 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 GLN E 567 GLN C 255 GLN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN F 508 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 19266 Z= 0.334 Angle : 0.681 8.273 26172 Z= 0.349 Chirality : 0.049 0.343 2952 Planarity : 0.004 0.072 3315 Dihedral : 7.616 48.667 3141 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.10 % Allowed : 2.36 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.18), residues: 2340 helix: 1.19 (0.39), residues: 165 sheet: -0.78 (0.17), residues: 930 loop : -0.84 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 114 HIS 0.006 0.001 HIS J 35 PHE 0.017 0.002 PHE M 71 TYR 0.023 0.002 TYR K 86 ARG 0.014 0.001 ARG H 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 566 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8278 (t70) cc_final: 0.8059 (t70) REVERT: A 117 ASP cc_start: 0.8670 (p0) cc_final: 0.8399 (p0) REVERT: H 57 LYS cc_start: 0.9461 (tptt) cc_final: 0.9176 (ttpt) REVERT: H 101 LEU cc_start: 0.8895 (tp) cc_final: 0.8241 (mt) REVERT: H 114 TYR cc_start: 0.6358 (m-10) cc_final: 0.5725 (m-10) REVERT: H 115 TYR cc_start: 0.8871 (m-10) cc_final: 0.8545 (m-10) REVERT: K 46 LEU cc_start: 0.9046 (pt) cc_final: 0.8815 (pt) REVERT: D 512 ASN cc_start: 0.9102 (t0) cc_final: 0.8809 (t0) REVERT: D 532 ILE cc_start: 0.9290 (mt) cc_final: 0.9022 (pt) REVERT: D 564 GLU cc_start: 0.7891 (mp0) cc_final: 0.7680 (mp0) REVERT: D 565 THR cc_start: 0.9276 (p) cc_final: 0.8931 (t) REVERT: D 592 PHE cc_start: 0.8333 (t80) cc_final: 0.7950 (t80) REVERT: Q 79 LEU cc_start: 0.8012 (mt) cc_final: 0.7565 (mt) REVERT: N 15 SER cc_start: 0.8897 (m) cc_final: 0.8066 (p) REVERT: N 112 ASP cc_start: 0.8780 (p0) cc_final: 0.8511 (p0) REVERT: B 62 GLN cc_start: 0.8787 (mt0) cc_final: 0.8402 (mt0) REVERT: B 117 ASP cc_start: 0.8813 (p0) cc_final: 0.8448 (p0) REVERT: B 240 THR cc_start: 0.9354 (m) cc_final: 0.8854 (p) REVERT: I 34 MET cc_start: 0.7716 (mmm) cc_final: 0.7150 (mmp) REVERT: I 59 PHE cc_start: 0.7149 (t80) cc_final: 0.6919 (t80) REVERT: I 76 LYS cc_start: 0.8817 (mtmm) cc_final: 0.8501 (ptpp) REVERT: I 80 TYR cc_start: 0.8185 (m-80) cc_final: 0.7139 (m-80) REVERT: I 115 TYR cc_start: 0.8357 (m-10) cc_final: 0.6916 (t80) REVERT: L 24 ARG cc_start: 0.7589 (mmm-85) cc_final: 0.7187 (mmm-85) REVERT: L 70 ASP cc_start: 0.7309 (t0) cc_final: 0.6809 (p0) REVERT: L 73 LEU cc_start: 0.8298 (tp) cc_final: 0.7981 (tp) REVERT: L 92 LYS cc_start: 0.8689 (tttt) cc_final: 0.8303 (tppt) REVERT: L 93 SER cc_start: 0.8676 (p) cc_final: 0.8385 (t) REVERT: L 104 LEU cc_start: 0.7702 (tp) cc_final: 0.7301 (tt) REVERT: E 555 ILE cc_start: 0.9110 (mt) cc_final: 0.8831 (mt) REVERT: E 565 THR cc_start: 0.9271 (p) cc_final: 0.8937 (t) REVERT: E 581 THR cc_start: 0.9598 (m) cc_final: 0.9282 (p) REVERT: E 591 ASP cc_start: 0.9120 (t0) cc_final: 0.8811 (t0) REVERT: E 592 PHE cc_start: 0.8352 (t80) cc_final: 0.7838 (t80) REVERT: R 61 ASP cc_start: 0.8496 (p0) cc_final: 0.7836 (t0) REVERT: R 76 ILE cc_start: 0.9266 (mp) cc_final: 0.8898 (tt) REVERT: R 106 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7389 (tm-30) REVERT: O 58 ASN cc_start: 0.8834 (t0) cc_final: 0.8321 (t0) REVERT: C 39 HIS cc_start: 0.8286 (t70) cc_final: 0.8002 (t70) REVERT: C 57 LEU cc_start: 0.9083 (tp) cc_final: 0.8694 (mp) REVERT: C 62 GLN cc_start: 0.8980 (mt0) cc_final: 0.8577 (mt0) REVERT: C 273 LEU cc_start: 0.7604 (mp) cc_final: 0.7284 (mp) REVERT: J 12 VAL cc_start: 0.6062 (t) cc_final: 0.5793 (t) REVERT: J 35 HIS cc_start: 0.8303 (m-70) cc_final: 0.8008 (m90) REVERT: J 46 GLU cc_start: 0.8860 (pt0) cc_final: 0.8335 (pm20) REVERT: J 55 ASP cc_start: 0.8115 (t70) cc_final: 0.7854 (t70) REVERT: J 82 GLN cc_start: 0.8046 (tp40) cc_final: 0.7733 (tp-100) REVERT: J 83 MET cc_start: 0.8782 (mtt) cc_final: 0.8433 (mmm) REVERT: J 86 LEU cc_start: 0.9096 (mt) cc_final: 0.8792 (mt) REVERT: J 101 LEU cc_start: 0.8919 (tp) cc_final: 0.8120 (mt) REVERT: J 102 GLN cc_start: 0.8172 (mt0) cc_final: 0.7483 (mt0) REVERT: M 60 SER cc_start: 0.9347 (p) cc_final: 0.9115 (t) REVERT: M 73 LEU cc_start: 0.8020 (tp) cc_final: 0.7524 (tp) REVERT: M 79 GLN cc_start: 0.6171 (pt0) cc_final: 0.5394 (pp30) REVERT: F 579 LEU cc_start: 0.9017 (mt) cc_final: 0.8797 (tp) REVERT: F 581 THR cc_start: 0.9643 (m) cc_final: 0.9317 (p) REVERT: F 592 PHE cc_start: 0.8230 (t80) cc_final: 0.7810 (t80) REVERT: S 4 LEU cc_start: 0.8457 (mt) cc_final: 0.8218 (mt) REVERT: S 18 ARG cc_start: 0.8770 (ttp80) cc_final: 0.8220 (ttp80) REVERT: S 20 THR cc_start: 0.8509 (p) cc_final: 0.8105 (p) REVERT: S 96 LEU cc_start: 0.9457 (mp) cc_final: 0.9215 (tt) REVERT: P 15 SER cc_start: 0.8831 (m) cc_final: 0.8305 (p) REVERT: P 52 HIS cc_start: 0.8009 (t-90) cc_final: 0.7734 (t70) REVERT: P 60 ASN cc_start: 0.9315 (t0) cc_final: 0.8890 (t0) REVERT: P 111 MET cc_start: 0.8617 (mtm) cc_final: 0.8054 (mtt) REVERT: P 112 ASP cc_start: 0.8885 (p0) cc_final: 0.8551 (p0) outliers start: 2 outliers final: 0 residues processed: 568 average time/residue: 0.2976 time to fit residues: 256.0388 Evaluate side-chains 446 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.0970 chunk 198 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 129 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 220 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 567 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN B 255 GLN I 31 ASN I 74 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 GLN ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19266 Z= 0.326 Angle : 0.675 10.711 26172 Z= 0.343 Chirality : 0.048 0.361 2952 Planarity : 0.004 0.055 3315 Dihedral : 7.209 41.745 3141 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.18), residues: 2340 helix: 1.23 (0.39), residues: 165 sheet: -0.73 (0.17), residues: 924 loop : -0.81 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 114 HIS 0.005 0.001 HIS I 112 PHE 0.012 0.002 PHE I 50 TYR 0.027 0.002 TYR I 114 ARG 0.009 0.000 ARG H 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 551 time to evaluate : 3.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8337 (t70) cc_final: 0.8125 (t70) REVERT: A 117 ASP cc_start: 0.8630 (p0) cc_final: 0.8383 (p0) REVERT: H 101 LEU cc_start: 0.8840 (tp) cc_final: 0.8113 (mt) REVERT: H 114 TYR cc_start: 0.6285 (m-10) cc_final: 0.5605 (m-10) REVERT: H 115 TYR cc_start: 0.8887 (m-10) cc_final: 0.8576 (m-10) REVERT: K 46 LEU cc_start: 0.9090 (pt) cc_final: 0.8857 (pt) REVERT: D 512 ASN cc_start: 0.9028 (t0) cc_final: 0.8714 (t0) REVERT: D 565 THR cc_start: 0.9261 (p) cc_final: 0.8949 (t) REVERT: D 592 PHE cc_start: 0.8307 (t80) cc_final: 0.7906 (t80) REVERT: Q 34 PHE cc_start: 0.8215 (m-80) cc_final: 0.7951 (m-10) REVERT: Q 61 ASP cc_start: 0.8095 (p0) cc_final: 0.7697 (p0) REVERT: N 15 SER cc_start: 0.8890 (m) cc_final: 0.8014 (p) REVERT: B 62 GLN cc_start: 0.8781 (mt0) cc_final: 0.8376 (mt0) REVERT: B 117 ASP cc_start: 0.8813 (p0) cc_final: 0.8519 (p0) REVERT: B 240 THR cc_start: 0.9450 (m) cc_final: 0.9065 (p) REVERT: I 59 PHE cc_start: 0.7275 (t80) cc_final: 0.6988 (t80) REVERT: I 76 LYS cc_start: 0.8793 (mtmm) cc_final: 0.8437 (ptpp) REVERT: I 80 TYR cc_start: 0.8230 (m-80) cc_final: 0.6869 (m-80) REVERT: L 24 ARG cc_start: 0.7439 (mmm-85) cc_final: 0.7058 (mmm-85) REVERT: L 70 ASP cc_start: 0.7293 (t0) cc_final: 0.6663 (p0) REVERT: L 73 LEU cc_start: 0.8354 (tp) cc_final: 0.7999 (tp) REVERT: L 92 LYS cc_start: 0.8714 (tttt) cc_final: 0.8467 (tppt) REVERT: L 104 LEU cc_start: 0.7699 (tp) cc_final: 0.7262 (tt) REVERT: E 555 ILE cc_start: 0.9200 (mt) cc_final: 0.8914 (mt) REVERT: E 565 THR cc_start: 0.9254 (p) cc_final: 0.8938 (t) REVERT: E 581 THR cc_start: 0.9615 (m) cc_final: 0.9286 (p) REVERT: E 591 ASP cc_start: 0.9143 (t0) cc_final: 0.8932 (t0) REVERT: E 592 PHE cc_start: 0.8340 (t80) cc_final: 0.7815 (t80) REVERT: R 76 ILE cc_start: 0.9260 (mp) cc_final: 0.8893 (tt) REVERT: R 78 ARG cc_start: 0.8966 (mtt-85) cc_final: 0.8765 (ttp-170) REVERT: R 96 LEU cc_start: 0.9416 (mp) cc_final: 0.9136 (tt) REVERT: R 106 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7411 (tm-30) REVERT: O 45 LEU cc_start: 0.8964 (mt) cc_final: 0.8705 (mt) REVERT: O 58 ASN cc_start: 0.8848 (t0) cc_final: 0.8402 (t0) REVERT: C 39 HIS cc_start: 0.8294 (t70) cc_final: 0.8035 (t70) REVERT: C 57 LEU cc_start: 0.9110 (tp) cc_final: 0.8641 (mp) REVERT: C 62 GLN cc_start: 0.8962 (mt0) cc_final: 0.8551 (mt0) REVERT: J 12 VAL cc_start: 0.6097 (t) cc_final: 0.5787 (t) REVERT: J 35 HIS cc_start: 0.8398 (m-70) cc_final: 0.8047 (m170) REVERT: J 46 GLU cc_start: 0.8824 (pt0) cc_final: 0.8331 (pm20) REVERT: J 83 MET cc_start: 0.8754 (mtt) cc_final: 0.8464 (mmm) REVERT: J 101 LEU cc_start: 0.9061 (tp) cc_final: 0.8034 (mt) REVERT: J 102 GLN cc_start: 0.8215 (mt0) cc_final: 0.7691 (mt0) REVERT: M 55 GLN cc_start: 0.7533 (tm-30) cc_final: 0.7299 (tm-30) REVERT: M 60 SER cc_start: 0.9346 (p) cc_final: 0.9117 (t) REVERT: M 73 LEU cc_start: 0.8004 (tp) cc_final: 0.7520 (tp) REVERT: M 79 GLN cc_start: 0.6191 (pt0) cc_final: 0.5414 (pp30) REVERT: F 512 ASN cc_start: 0.9226 (t0) cc_final: 0.9012 (t0) REVERT: F 581 THR cc_start: 0.9668 (m) cc_final: 0.9327 (p) REVERT: F 592 PHE cc_start: 0.8255 (t80) cc_final: 0.7857 (t80) REVERT: S 4 LEU cc_start: 0.8442 (mt) cc_final: 0.8195 (mt) REVERT: S 18 ARG cc_start: 0.8789 (ttp80) cc_final: 0.8327 (ttp80) REVERT: S 20 THR cc_start: 0.8544 (p) cc_final: 0.8215 (p) REVERT: P 15 SER cc_start: 0.8847 (m) cc_final: 0.8375 (p) REVERT: P 32 TYR cc_start: 0.8793 (m-10) cc_final: 0.8487 (m-10) REVERT: P 52 HIS cc_start: 0.7961 (t-90) cc_final: 0.7692 (t70) REVERT: P 60 ASN cc_start: 0.9357 (t0) cc_final: 0.8967 (t0) REVERT: P 111 MET cc_start: 0.8563 (mtm) cc_final: 0.8030 (mtt) outliers start: 0 outliers final: 0 residues processed: 551 average time/residue: 0.2960 time to fit residues: 247.7144 Evaluate side-chains 437 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.0221 > 50: distance: 33 - 39: 20.613 distance: 39 - 40: 16.556 distance: 40 - 41: 16.217 distance: 40 - 43: 6.216 distance: 41 - 42: 18.119 distance: 41 - 45: 20.335 distance: 43 - 44: 12.722 distance: 44 - 118: 9.396 distance: 45 - 46: 20.759 distance: 46 - 47: 7.045 distance: 46 - 49: 17.937 distance: 47 - 48: 10.491 distance: 47 - 53: 5.663 distance: 49 - 50: 18.476 distance: 50 - 51: 18.844 distance: 50 - 52: 18.210 distance: 53 - 54: 9.756 distance: 53 - 59: 16.522 distance: 54 - 57: 17.355 distance: 55 - 56: 17.479 distance: 55 - 60: 13.410 distance: 57 - 58: 20.141 distance: 58 - 59: 14.832 distance: 60 - 61: 29.958 distance: 61 - 62: 23.586 distance: 61 - 64: 16.875 distance: 62 - 63: 14.361 distance: 62 - 65: 21.537 distance: 65 - 66: 13.175 distance: 66 - 67: 7.305 distance: 66 - 69: 7.628 distance: 67 - 68: 31.173 distance: 67 - 70: 11.906 distance: 70 - 71: 13.563 distance: 70 - 76: 27.226 distance: 71 - 72: 10.761 distance: 71 - 74: 5.583 distance: 72 - 73: 14.758 distance: 72 - 77: 30.012 distance: 74 - 75: 16.964 distance: 75 - 76: 44.365 distance: 77 - 78: 19.904 distance: 78 - 79: 7.553 distance: 78 - 81: 8.262 distance: 79 - 80: 9.141 distance: 79 - 85: 14.751 distance: 81 - 82: 3.139 distance: 82 - 83: 18.182 distance: 82 - 84: 35.520 distance: 85 - 86: 30.615 distance: 86 - 87: 22.558 distance: 87 - 88: 18.585 distance: 87 - 89: 11.994 distance: 89 - 90: 14.172 distance: 90 - 91: 7.579 distance: 90 - 93: 12.102 distance: 91 - 92: 13.358 distance: 91 - 97: 19.380 distance: 93 - 94: 15.662 distance: 93 - 95: 15.254 distance: 94 - 96: 23.436 distance: 97 - 98: 5.015 distance: 98 - 99: 13.736 distance: 98 - 101: 10.186 distance: 99 - 100: 18.097 distance: 101 - 102: 28.034 distance: 102 - 103: 14.617 distance: 103 - 104: 7.249 distance: 104 - 105: 20.252 distance: 105 - 106: 18.849 distance: 105 - 107: 19.926