Starting phenix.real_space_refine on Tue Apr 9 07:27:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy2_11547/04_2024/6zy2_11547.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy2_11547/04_2024/6zy2_11547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy2_11547/04_2024/6zy2_11547.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy2_11547/04_2024/6zy2_11547.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy2_11547/04_2024/6zy2_11547.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy2_11547/04_2024/6zy2_11547.pdb" } resolution = 3.6 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 76 5.16 5 C 10127 2.51 5 N 2651 2.21 5 O 2864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 7": "OE1" <-> "OE2" Residue "D ASP 95": "OD1" <-> "OD2" Residue "D ASP 130": "OD1" <-> "OD2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "I PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 70": "OD1" <-> "OD2" Residue "I TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 74": "OD1" <-> "OD2" Residue "J TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 7": "OE1" <-> "OE2" Residue "K PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 70": "OD1" <-> "OD2" Residue "K ASP 132": "OD1" <-> "OD2" Residue "K GLU 144": "OE1" <-> "OE2" Residue "K TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 47": "OD1" <-> "OD2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B ASP 63": "OD1" <-> "OD2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "C ASP 21": "OD1" <-> "OD2" Residue "C ASP 79": "OD1" <-> "OD2" Residue "F ASP 13": "OD1" <-> "OD2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 135": "NH1" <-> "NH2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F GLU 170": "OE1" <-> "OE2" Residue "F ASP 176": "OD1" <-> "OD2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F ASP 249": "OD1" <-> "OD2" Residue "F ARG 255": "NH1" <-> "NH2" Residue "F TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 260": "OD1" <-> "OD2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 33": "NH1" <-> "NH2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 99": "OD1" <-> "OD2" Residue "G GLU 112": "OE1" <-> "OE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 157": "NH1" <-> "NH2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G ASP 176": "OD1" <-> "OD2" Residue "G ASP 220": "OD1" <-> "OD2" Residue "G ASP 245": "OD1" <-> "OD2" Residue "G ARG 255": "NH1" <-> "NH2" Residue "E ASP 138": "OD1" <-> "OD2" Residue "E PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 198": "OD1" <-> "OD2" Residue "H GLU 36": "OE1" <-> "OE2" Residue "H ASP 223": "OD1" <-> "OD2" Residue "H ASP 250": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15718 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1059 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain breaks: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 55 Chain: "D" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1068 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1027 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1065 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "K" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1094 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1058 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 734 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "C" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1984 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 18, 'TRANS': 242} Chain: "G" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1989 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 18, 'TRANS': 243} Chain: "E" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1948 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 251} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1949 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 7, 'TRANS': 251} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.53, per 1000 atoms: 0.54 Number of scatterers: 15718 At special positions: 0 Unit cell: (98.358, 125.736, 142.974, 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 76 16.00 O 2864 8.00 N 2651 7.00 C 10127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 5.44 Conformation dependent library (CDL) restraints added in 3.0 seconds 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3836 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 23 sheets defined 39.1% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 2 through 27 removed outlier: 3.555A pdb=" N GLU A 7 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE A 8 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP A 9 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 27 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 152 removed outlier: 3.905A pdb=" N LEU A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 25 removed outlier: 3.507A pdb=" N VAL D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 147 removed outlier: 3.741A pdb=" N ILE D 147 " --> pdb=" O LEU D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'I' and resid 7 through 25 removed outlier: 3.604A pdb=" N GLY I 11 " --> pdb=" O GLU I 7 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE I 12 " --> pdb=" O ILE I 8 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE I 13 " --> pdb=" O TRP I 9 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA I 16 " --> pdb=" O ILE I 12 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 151 removed outlier: 4.100A pdb=" N GLY I 148 " --> pdb=" O GLU I 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 29 removed outlier: 3.880A pdb=" N TRP J 9 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL J 10 " --> pdb=" O ASN J 6 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA J 21 " --> pdb=" O ALA J 17 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU J 26 " --> pdb=" O LEU J 22 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS J 27 " --> pdb=" O PHE J 23 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA J 29 " --> pdb=" O CYS J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 152 removed outlier: 4.050A pdb=" N LEU J 151 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 20 removed outlier: 4.187A pdb=" N ASN K 6 " --> pdb=" O GLN K 2 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU K 7 " --> pdb=" O THR K 3 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE K 8 " --> pdb=" O LYS K 4 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP K 9 " --> pdb=" O LYS K 5 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL K 10 " --> pdb=" O ASN K 6 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY K 11 " --> pdb=" O GLU K 7 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE K 12 " --> pdb=" O ILE K 8 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE K 13 " --> pdb=" O TRP K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 152 removed outlier: 3.760A pdb=" N LEU K 151 " --> pdb=" O ILE K 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 19 removed outlier: 3.588A pdb=" N VAL L 10 " --> pdb=" O ASN L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 152 removed outlier: 3.582A pdb=" N LEU L 146 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE L 147 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY L 148 " --> pdb=" O GLU L 144 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE L 150 " --> pdb=" O LEU L 146 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU L 151 " --> pdb=" O ILE L 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 31 removed outlier: 3.580A pdb=" N GLU B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 39 removed outlier: 3.752A pdb=" N GLY B 38 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE B 39 " --> pdb=" O VAL B 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 35 through 39' Processing helix chain 'B' and resid 51 through 67 removed outlier: 3.859A pdb=" N ALA B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS B 67 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 88 removed outlier: 3.606A pdb=" N TYR B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B 86 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.562A pdb=" N GLU C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.812A pdb=" N LEU C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU C 58 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C 67 " --> pdb=" O ASP C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 88 removed outlier: 4.072A pdb=" N TYR C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 84 " --> pdb=" O LYS C 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 56 Processing helix chain 'F' and resid 79 through 87 removed outlier: 3.664A pdb=" N ARG F 84 " --> pdb=" O TYR F 81 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS F 85 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET F 87 " --> pdb=" O ARG F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 107 removed outlier: 3.627A pdb=" N VAL F 106 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA F 107 " --> pdb=" O PHE F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 125 removed outlier: 3.630A pdb=" N HIS F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER F 123 " --> pdb=" O PRO F 119 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 133 removed outlier: 4.018A pdb=" N VAL F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 145 removed outlier: 3.517A pdb=" N LEU F 145 " --> pdb=" O PRO F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 159 removed outlier: 3.694A pdb=" N ARG F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA F 153 " --> pdb=" O MET F 149 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA F 154 " --> pdb=" O ALA F 150 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU F 155 " --> pdb=" O ARG F 151 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA F 156 " --> pdb=" O ARG F 152 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG F 157 " --> pdb=" O ALA F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 193 removed outlier: 3.741A pdb=" N VAL F 182 " --> pdb=" O ILE F 178 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL F 184 " --> pdb=" O MET F 180 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS F 185 " --> pdb=" O GLY F 181 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE F 187 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER F 192 " --> pdb=" O SER F 188 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 209 removed outlier: 3.793A pdb=" N VAL F 208 " --> pdb=" O ASP F 204 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU F 209 " --> pdb=" O VAL F 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 204 through 209' Processing helix chain 'F' and resid 240 through 244 Processing helix chain 'F' and resid 260 through 266 removed outlier: 3.718A pdb=" N ASP F 264 " --> pdb=" O ASP F 260 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU F 266 " --> pdb=" O HIS F 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 56 removed outlier: 4.314A pdb=" N LEU G 51 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG G 52 " --> pdb=" O THR G 48 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU G 53 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 85 removed outlier: 3.743A pdb=" N TYR G 81 " --> pdb=" O ARG G 77 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR G 82 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL G 83 " --> pdb=" O ARG G 79 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS G 85 " --> pdb=" O TYR G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 107 removed outlier: 4.039A pdb=" N ALA G 107 " --> pdb=" O PHE G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 130 removed outlier: 3.782A pdb=" N HIS G 122 " --> pdb=" O ALA G 118 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER G 123 " --> pdb=" O PRO G 119 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL G 125 " --> pdb=" O LEU G 121 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET G 126 " --> pdb=" O HIS G 122 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU G 130 " --> pdb=" O MET G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 145 Processing helix chain 'G' and resid 146 through 154 removed outlier: 3.696A pdb=" N ARG G 151 " --> pdb=" O GLY G 147 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG G 152 " --> pdb=" O GLY G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 159 removed outlier: 3.632A pdb=" N ILE G 159 " --> pdb=" O LEU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 195 removed outlier: 3.698A pdb=" N GLY G 181 " --> pdb=" O PRO G 177 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL G 182 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER G 188 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER G 192 " --> pdb=" O SER G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 244 removed outlier: 3.847A pdb=" N PHE G 243 " --> pdb=" O ARG G 239 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU G 244 " --> pdb=" O VAL G 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 239 through 244' Processing helix chain 'G' and resid 260 through 265 removed outlier: 3.509A pdb=" N ASP G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU G 265 " --> pdb=" O TYR G 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 260 through 265' Processing helix chain 'E' and resid 6 through 29 removed outlier: 3.612A pdb=" N GLY E 10 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS E 11 " --> pdb=" O ALA E 7 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS E 12 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS E 15 " --> pdb=" O HIS E 11 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E 17 " --> pdb=" O GLY E 13 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE E 20 " --> pdb=" O THR E 16 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA E 23 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 51 removed outlier: 4.079A pdb=" N VAL E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN E 50 " --> pdb=" O ARG E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 removed outlier: 3.786A pdb=" N ILE E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 60 " --> pdb=" O MET E 56 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL E 64 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE E 65 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY E 71 " --> pdb=" O GLY E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 95 removed outlier: 3.849A pdb=" N ALA E 92 " --> pdb=" O GLY E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 112 removed outlier: 3.572A pdb=" N VAL E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA E 105 " --> pdb=" O PRO E 101 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 107 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 126 removed outlier: 3.642A pdb=" N THR E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR E 126 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 134 Processing helix chain 'E' and resid 144 through 153 removed outlier: 3.575A pdb=" N TRP E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY E 151 " --> pdb=" O ARG E 147 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE E 153 " --> pdb=" O TRP E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 168 removed outlier: 3.748A pdb=" N VAL E 160 " --> pdb=" O PRO E 156 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.691A pdb=" N ALA E 188 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET E 189 " --> pdb=" O TRP E 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 185 through 189' Processing helix chain 'E' and resid 199 through 220 removed outlier: 4.003A pdb=" N VAL E 213 " --> pdb=" O PHE E 209 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE E 216 " --> pdb=" O THR E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 256 removed outlier: 3.947A pdb=" N ILE E 231 " --> pdb=" O THR E 227 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER E 232 " --> pdb=" O SER E 228 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 249 " --> pdb=" O ALA E 245 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP E 250 " --> pdb=" O VAL E 246 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL E 252 " --> pdb=" O GLY E 248 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU E 256 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 32 removed outlier: 3.639A pdb=" N GLY H 13 " --> pdb=" O LEU H 9 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE H 14 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS H 15 " --> pdb=" O HIS H 11 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY H 24 " --> pdb=" O PHE H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 47 removed outlier: 3.933A pdb=" N VAL H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 78 removed outlier: 4.074A pdb=" N ILE H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL H 64 " --> pdb=" O VAL H 60 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE H 65 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU H 70 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU H 72 " --> pdb=" O MET H 68 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR H 75 " --> pdb=" O GLY H 71 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU H 76 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL H 77 " --> pdb=" O GLN H 73 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU H 78 " --> pdb=" O GLY H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 86 Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.579A pdb=" N ALA H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 126 removed outlier: 3.706A pdb=" N GLY H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY H 113 " --> pdb=" O ALA H 109 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER H 114 " --> pdb=" O GLY H 110 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA H 115 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR H 117 " --> pdb=" O GLY H 113 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE H 120 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR H 126 " --> pdb=" O LEU H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 removed outlier: 3.590A pdb=" N MET H 132 " --> pdb=" O GLN H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 136 removed outlier: 3.801A pdb=" N ALA H 136 " --> pdb=" O GLU H 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 133 through 136' Processing helix chain 'H' and resid 138 through 143 removed outlier: 3.559A pdb=" N VAL H 143 " --> pdb=" O PRO H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 153 removed outlier: 3.576A pdb=" N TRP H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY H 151 " --> pdb=" O ARG H 147 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE H 153 " --> pdb=" O TRP H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 175 removed outlier: 3.836A pdb=" N VAL H 160 " --> pdb=" O PRO H 156 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 223 removed outlier: 3.533A pdb=" N LEU H 203 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL H 207 " --> pdb=" O LEU H 203 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL H 208 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR H 212 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL H 213 " --> pdb=" O PHE H 209 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE H 216 " --> pdb=" O THR H 212 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY H 221 " --> pdb=" O SER H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 247 removed outlier: 3.892A pdb=" N ILE H 231 " --> pdb=" O THR H 227 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER H 232 " --> pdb=" O SER H 228 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR H 236 " --> pdb=" O SER H 232 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR H 238 " --> pdb=" O ALA H 234 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL H 239 " --> pdb=" O THR H 235 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL H 240 " --> pdb=" O THR H 236 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU H 247 " --> pdb=" O SER H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 256 removed outlier: 3.873A pdb=" N ALA H 255 " --> pdb=" O PHE H 251 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU H 256 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 45 removed outlier: 3.959A pdb=" N TYR A 40 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE A 86 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 66 removed outlier: 6.979A pdb=" N VAL A 58 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 99 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 81 through 86 removed outlier: 3.765A pdb=" N THR D 83 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASP D 70 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU D 85 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL D 68 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE D 60 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY D 66 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU D 114 " --> pdb=" O PRO D 57 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N SER D 59 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 68 through 73 removed outlier: 6.302A pdb=" N VAL I 68 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLU I 85 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP I 70 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR I 83 " --> pdb=" O ASP I 70 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N ILE I 134 " --> pdb=" O THR I 41 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N TYR I 43 " --> pdb=" O ILE I 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 58 through 59 removed outlier: 6.884A pdb=" N VAL I 58 " --> pdb=" O VAL I 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 99 through 103 Processing sheet with id=AA7, first strand: chain 'J' and resid 39 through 41 Processing sheet with id=AA8, first strand: chain 'J' and resid 39 through 41 removed outlier: 3.682A pdb=" N THR J 83 " --> pdb=" O ASP J 70 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP J 70 " --> pdb=" O THR J 83 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLU J 85 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL J 68 " --> pdb=" O GLU J 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 63 through 66 removed outlier: 6.004A pdb=" N VAL J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE J 60 " --> pdb=" O VAL J 64 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY J 66 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER J 59 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER J 98 " --> pdb=" O ASN J 115 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 71 through 73 removed outlier: 7.206A pdb=" N TYR K 43 " --> pdb=" O ILE K 134 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 85 through 86 removed outlier: 3.929A pdb=" N ARG K 67 " --> pdb=" O GLU K 85 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL K 64 " --> pdb=" O ILE K 60 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE K 60 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY K 66 " --> pdb=" O VAL K 58 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER K 59 " --> pdb=" O LEU K 114 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA K 113 " --> pdb=" O SER K 100 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER K 100 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU K 99 " --> pdb=" O LYS K 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 39 through 41 removed outlier: 4.172A pdb=" N ASP L 70 " --> pdb=" O THR L 83 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLU L 85 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL L 68 " --> pdb=" O GLU L 85 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 39 through 41 removed outlier: 3.616A pdb=" N ALA L 44 " --> pdb=" O VAL L 82 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR L 43 " --> pdb=" O ILE L 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 64 through 66 removed outlier: 6.668A pdb=" N VAL L 64 " --> pdb=" O ILE L 60 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE L 60 " --> pdb=" O VAL L 64 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG L 102 " --> pdb=" O TYR L 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 6 through 10 removed outlier: 4.106A pdb=" N MET B 8 " --> pdb=" O ALA B 15 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA B 15 " --> pdb=" O MET B 8 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 10 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL B 47 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY B 18 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ARG B 49 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 20 " --> pdb=" O ARG B 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.784A pdb=" N ILE B 42 " --> pdb=" O GLN B 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 41 through 43 removed outlier: 3.518A pdb=" N GLN C 75 " --> pdb=" O ILE C 42 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 27 through 30 removed outlier: 3.906A pdb=" N VAL F 14 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU F 29 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ARG F 12 " --> pdb=" O LEU F 29 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 165 through 168 removed outlier: 3.570A pdb=" N HIS F 214 " --> pdb=" O ILE F 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 218 through 219 Processing sheet with id=AC3, first strand: chain 'G' and resid 16 through 17 Processing sheet with id=AC4, first strand: chain 'G' and resid 165 through 168 removed outlier: 3.521A pdb=" N LEU G 218 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE G 217 " --> pdb=" O VAL G 224 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 66 through 67 439 hydrogen bonds defined for protein. 1245 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: 3.97 Time building geometry restraints manager: 6.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5065 1.35 - 1.46: 3453 1.46 - 1.58: 7330 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 15986 Sorted by residual: bond pdb=" C ILE F 72 " pdb=" N PRO F 73 " ideal model delta sigma weight residual 1.331 1.379 -0.047 7.90e-03 1.60e+04 3.60e+01 bond pdb=" C VAL F 205 " pdb=" N PRO F 206 " ideal model delta sigma weight residual 1.334 1.383 -0.049 8.40e-03 1.42e+04 3.43e+01 bond pdb=" N THR J 3 " pdb=" CA THR J 3 " ideal model delta sigma weight residual 1.460 1.485 -0.026 1.54e-02 4.22e+03 2.75e+00 bond pdb=" N ASP F 245 " pdb=" CA ASP F 245 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.32e-02 5.74e+03 2.28e+00 bond pdb=" N ASP F 68 " pdb=" CA ASP F 68 " ideal model delta sigma weight residual 1.460 1.482 -0.022 1.54e-02 4.22e+03 2.10e+00 ... (remaining 15981 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.34: 530 107.34 - 114.40: 9673 114.40 - 121.46: 7355 121.46 - 128.51: 4071 128.51 - 135.57: 99 Bond angle restraints: 21728 Sorted by residual: angle pdb=" C LEU F 244 " pdb=" N ASP F 245 " pdb=" CA ASP F 245 " ideal model delta sigma weight residual 121.31 128.62 -7.31 1.49e+00 4.50e-01 2.41e+01 angle pdb=" C GLN J 2 " pdb=" N THR J 3 " pdb=" CA THR J 3 " ideal model delta sigma weight residual 122.46 128.42 -5.96 1.41e+00 5.03e-01 1.78e+01 angle pdb=" C ASP F 220 " pdb=" N LYS F 221 " pdb=" CA LYS F 221 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C GLY C 11 " pdb=" N ASP C 12 " pdb=" CA ASP C 12 " ideal model delta sigma weight residual 121.54 128.82 -7.28 1.91e+00 2.74e-01 1.45e+01 angle pdb=" C PRO F 171 " pdb=" N PHE F 172 " pdb=" CA PHE F 172 " ideal model delta sigma weight residual 122.46 127.64 -5.18 1.41e+00 5.03e-01 1.35e+01 ... (remaining 21723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 8811 17.24 - 34.48: 600 34.48 - 51.71: 121 51.71 - 68.95: 9 68.95 - 86.19: 7 Dihedral angle restraints: 9548 sinusoidal: 3588 harmonic: 5960 Sorted by residual: dihedral pdb=" CA ASP F 245 " pdb=" C ASP F 245 " pdb=" N GLY F 246 " pdb=" CA GLY F 246 " ideal model delta harmonic sigma weight residual 180.00 -157.31 -22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA VAL F 205 " pdb=" C VAL F 205 " pdb=" N PRO F 206 " pdb=" CA PRO F 206 " ideal model delta harmonic sigma weight residual -180.00 -163.01 -16.99 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ASP J 74 " pdb=" CB ASP J 74 " pdb=" CG ASP J 74 " pdb=" OD1 ASP J 74 " ideal model delta sinusoidal sigma weight residual -30.00 -86.46 56.46 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 9545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1959 0.044 - 0.088: 504 0.088 - 0.132: 160 0.132 - 0.176: 23 0.176 - 0.220: 5 Chirality restraints: 2651 Sorted by residual: chirality pdb=" CB ILE K 93 " pdb=" CA ILE K 93 " pdb=" CG1 ILE K 93 " pdb=" CG2 ILE K 93 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE A 71 " pdb=" CA ILE A 71 " pdb=" CG1 ILE A 71 " pdb=" CG2 ILE A 71 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.85e-01 chirality pdb=" CB VAL K 31 " pdb=" CA VAL K 31 " pdb=" CG1 VAL K 31 " pdb=" CG2 VAL K 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.52e-01 ... (remaining 2648 not shown) Planarity restraints: 2720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 155 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO E 156 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 156 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 156 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 155 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO H 156 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO H 156 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 156 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 205 " 0.035 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO G 206 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO G 206 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 206 " 0.029 5.00e-02 4.00e+02 ... (remaining 2717 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4854 2.83 - 3.34: 12105 3.34 - 3.86: 24099 3.86 - 4.38: 26329 4.38 - 4.90: 46362 Nonbonded interactions: 113749 Sorted by model distance: nonbonded pdb=" O ASP H 250 " pdb=" OG1 THR H 254 " model vdw 2.308 2.440 nonbonded pdb=" O LEU E 155 " pdb=" OG1 THR E 159 " model vdw 2.312 2.440 nonbonded pdb=" O ASP B 79 " pdb=" OG1 THR B 83 " model vdw 2.338 2.440 nonbonded pdb=" O ALA E 234 " pdb=" OG1 THR E 238 " model vdw 2.342 2.440 nonbonded pdb=" OG SER F 123 " pdb=" O LEU G 265 " model vdw 2.345 2.440 ... (remaining 113744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 25 or (resid 26 through 29 and (name N or name CA \ or name C or name O or name CB )) or resid 38 or resid 40 through 80 or (resid \ 81 and (name N or name CA or name C or name O or name CB )) or resid 82 through \ 85 or (resid 86 through 87 and (name N or name CA or name C or name O or name CB \ )) or resid 88 or (resid 89 through 90 and (name N or name CA or name C or name \ O or name CB )) or resid 91 through 96 or (resid 97 through 98 and (name N or n \ ame CA or name C or name O or name CB )) or resid 99 through 108 or (resid 109 a \ nd (name N or name CA or name C or name O or name CB )) or resid 110 through 111 \ or (resid 112 through 113 and (name N or name CA or name C or name O or name CB \ )) or resid 114 through 115 or (resid 126 through 130 and (name N or name CA or \ name C or name O or name CB )) or resid 131 or (resid 132 and (name N or name C \ A or name C or name O or name CB )) or resid 133 through 136 or (resid 137 and ( \ name N or name CA or name C or name O or name CB )) or resid 138 through 140 or \ (resid 141 and (name N or name CA or name C or name O or name CB )) or resid 142 \ or (resid 143 through 144 and (name N or name CA or name C or name O or name CB \ )) or resid 145 through 146 or (resid 147 and (name N or name CA or name C or n \ ame O or name CB )) or resid 148 through 152)) selection = (chain 'D' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 25 or (resid 26 through 29 and (name N or name CA \ or name C or name O or name CB )) or resid 38 or resid 40 through 46 or (resid \ 47 and (name N or name CA or name C or name O or name CB )) or resid 48 through \ 54 or (resid 55 and (name N or name CA or name C or name O or name CB )) or resi \ d 56 through 59 or (resid 60 and (name N or name CA or name C or name O or name \ CB )) or resid 61 through 62 or (resid 63 and (name N or name CA or name C or na \ me O or name CB )) or resid 64 or (resid 65 and (name N or name CA or name C or \ name O or name CB )) or resid 66 or (resid 67 and (name N or name CA or name C o \ r name O or name CB )) or resid 68 through 73 or (resid 74 and (name N or name C \ A or name C or name O or name CB )) or resid 75 or (resid 76 through 77 and (nam \ e N or name CA or name C or name O or name CB )) or resid 78 through 84 or (resi \ d 85 through 87 and (name N or name CA or name C or name O or name CB )) or resi \ d 88 or (resid 89 through 90 and (name N or name CA or name C or name O or name \ CB )) or resid 91 through 95 or (resid 96 through 98 and (name N or name CA or n \ ame C or name O or name CB )) or resid 99 through 108 or (resid 109 and (name N \ or name CA or name C or name O or name CB )) or resid 110 through 111 or (resid \ 112 through 113 and (name N or name CA or name C or name O or name CB )) or resi \ d 114 through 115 or (resid 126 through 130 and (name N or name CA or name C or \ name O or name CB )) or resid 131 or (resid 132 and (name N or name CA or name C \ or name O or name CB )) or resid 133 through 136 or (resid 137 and (name N or n \ ame CA or name C or name O or name CB )) or resid 138 through 140 or (resid 141 \ and (name N or name CA or name C or name O or name CB )) or resid 142 or (resid \ 143 through 144 and (name N or name CA or name C or name O or name CB )) or resi \ d 145 through 146 or (resid 147 and (name N or name CA or name C or name O or na \ me CB )) or resid 148 through 152)) selection = (chain 'I' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 25 or (resid 26 through 29 and (name N or name CA \ or name C or name O or name CB )) or resid 38 or resid 40 through 46 or (resid \ 47 and (name N or name CA or name C or name O or name CB )) or resid 48 through \ 54 or (resid 55 and (name N or name CA or name C or name O or name CB )) or resi \ d 56 through 59 or (resid 60 and (name N or name CA or name C or name O or name \ CB )) or resid 61 through 62 or (resid 63 and (name N or name CA or name C or na \ me O or name CB )) or resid 64 or (resid 65 and (name N or name CA or name C or \ name O or name CB )) or resid 66 or (resid 67 and (name N or name CA or name C o \ r name O or name CB )) or resid 68 through 69 or (resid 70 and (name N or name C \ A or name C or name O or name CB )) or resid 71 through 73 or (resid 74 and (nam \ e N or name CA or name C or name O or name CB )) or resid 75 or (resid 76 throug \ h 77 and (name N or name CA or name C or name O or name CB )) or resid 78 throug \ h 80 or (resid 81 and (name N or name CA or name C or name O or name CB )) or re \ sid 82 through 84 or (resid 85 through 87 and (name N or name CA or name C or na \ me O or name CB )) or resid 88 or (resid 89 through 90 and (name N or name CA or \ name C or name O or name CB )) or resid 91 or (resid 92 and (name N or name CA \ or name C or name O or name CB )) or resid 93 through 95 or (resid 96 through 98 \ and (name N or name CA or name C or name O or name CB )) or resid 99 through 10 \ 8 or (resid 109 and (name N or name CA or name C or name O or name CB )) or resi \ d 110 through 111 or (resid 112 through 113 and (name N or name CA or name C or \ name O or name CB )) or resid 114 through 115 or (resid 126 through 130 and (nam \ e N or name CA or name C or name O or name CB )) or resid 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 through 142 or \ (resid 143 through 144 and (name N or name CA or name C or name O or name CB )) \ or resid 145 through 146 or (resid 147 and (name N or name CA or name C or name \ O or name CB )) or resid 148 through 152)) selection = (chain 'J' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 25 or (resid 26 through 29 and (name N or name CA \ or name C or name O or name CB )) or resid 38 or resid 40 through 46 or (resid \ 47 and (name N or name CA or name C or name O or name CB )) or resid 48 through \ 54 or (resid 55 and (name N or name CA or name C or name O or name CB )) or resi \ d 56 through 59 or (resid 60 and (name N or name CA or name C or name O or name \ CB )) or resid 61 through 62 or (resid 63 and (name N or name CA or name C or na \ me O or name CB )) or resid 64 or (resid 65 and (name N or name CA or name C or \ name O or name CB )) or resid 66 or (resid 67 and (name N or name CA or name C o \ r name O or name CB )) or resid 68 through 69 or (resid 70 and (name N or name C \ A or name C or name O or name CB )) or resid 71 through 73 or (resid 74 and (nam \ e N or name CA or name C or name O or name CB )) or resid 75 or (resid 76 throug \ h 77 and (name N or name CA or name C or name O or name CB )) or resid 78 throug \ h 80 or (resid 81 and (name N or name CA or name C or name O or name CB )) or re \ sid 82 through 84 or (resid 85 through 87 and (name N or name CA or name C or na \ me O or name CB )) or resid 88 through 89 or (resid 90 and (name N or name CA or \ name C or name O or name CB )) or resid 91 or (resid 92 and (name N or name CA \ or name C or name O or name CB )) or resid 93 through 108 or (resid 109 and (nam \ e N or name CA or name C or name O or name CB )) or resid 110 through 115 or (re \ sid 126 through 130 and (name N or name CA or name C or name O or name CB )) or \ resid 131 through 135 or (resid 136 through 137 and (name N or name CA or name C \ or name O or name CB )) or resid 138 through 140 or (resid 141 and (name N or n \ ame CA or name C or name O or name CB )) or resid 142 or (resid 143 through 144 \ and (name N or name CA or name C or name O or name CB )) or resid 145 through 15 \ 2)) selection = (chain 'K' and (resid 1 through 26 or (resid 27 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 38 through 46 or (resid 47 and (nam \ e N or name CA or name C or name O or name CB )) or resid 48 through 54 or (resi \ d 55 and (name N or name CA or name C or name O or name CB )) or resid 56 throug \ h 59 or (resid 60 and (name N or name CA or name C or name O or name CB )) or re \ sid 61 through 62 or (resid 63 and (name N or name CA or name C or name O or nam \ e CB )) or resid 64 or (resid 65 and (name N or name CA or name C or name O or n \ ame CB )) or resid 66 or (resid 67 and (name N or name CA or name C or name O or \ name CB )) or resid 68 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 73 or (resid 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 or (resid 76 through 77 and (n \ ame N or name CA or name C or name O or name CB )) or resid 78 through 80 or (re \ sid 81 and (name N or name CA or name C or name O or name CB )) or resid 82 thro \ ugh 84 or (resid 85 through 87 and (name N or name CA or name C or name O or nam \ e CB )) or resid 88 or (resid 89 through 90 and (name N or name CA or name C or \ name O or name CB )) or resid 91 or (resid 92 and (name N or name CA or name C o \ r name O or name CB )) or resid 93 through 95 or (resid 96 through 98 and (name \ N or name CA or name C or name O or name CB )) or resid 99 through 108 or (resid \ 109 and (name N or name CA or name C or name O or name CB )) or resid 110 throu \ gh 111 or (resid 112 through 113 and (name N or name CA or name C or name O or n \ ame CB )) or resid 114 through 115 or (resid 126 through 130 and (name N or name \ CA or name C or name O or name CB )) or resid 131 or (resid 132 and (name N or \ name CA or name C or name O or name CB )) or resid 133 through 136 or (resid 137 \ and (name N or name CA or name C or name O or name CB )) or resid 138 through 1 \ 40 or (resid 141 and (name N or name CA or name C or name O or name CB )) or res \ id 142 through 143 or (resid 144 and (name N or name CA or name C or name O or n \ ame CB )) or resid 145 through 146 or (resid 147 and (name N or name CA or name \ C or name O or name CB )) or resid 148 through 152)) selection = (chain 'L' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 25 or (resid 26 through 29 and (name N or name CA \ or name C or name O or name CB )) or resid 38 or resid 40 through 46 or (resid \ 47 and (name N or name CA or name C or name O or name CB )) or resid 48 through \ 54 or (resid 55 and (name N or name CA or name C or name O or name CB )) or resi \ d 56 through 59 or (resid 60 and (name N or name CA or name C or name O or name \ CB )) or resid 61 through 62 or (resid 63 and (name N or name CA or name C or na \ me O or name CB )) or resid 64 or (resid 65 and (name N or name CA or name C or \ name O or name CB )) or resid 66 or (resid 67 and (name N or name CA or name C o \ r name O or name CB )) or resid 68 through 73 or (resid 74 and (name N or name C \ A or name C or name O or name CB )) or resid 75 or (resid 76 through 77 and (nam \ e N or name CA or name C or name O or name CB )) or resid 78 through 80 or (resi \ d 81 and (name N or name CA or name C or name O or name CB )) or resid 82 throug \ h 86 or (resid 87 and (name N or name CA or name C or name O or name CB )) or re \ sid 88 or (resid 89 through 90 and (name N or name CA or name C or name O or nam \ e CB )) or resid 91 or (resid 92 and (name N or name CA or name C or name O or n \ ame CB )) or resid 93 through 95 or (resid 96 through 98 and (name N or name CA \ or name C or name O or name CB )) or resid 99 through 111 or (resid 112 through \ 113 and (name N or name CA or name C or name O or name CB )) or resid 114 throug \ h 115 or (resid 126 through 130 and (name N or name CA or name C or name O or na \ me CB )) or resid 131 through 135 or (resid 136 through 137 and (name N or name \ CA or name C or name O or name CB )) or resid 138 through 140 or (resid 141 and \ (name N or name CA or name C or name O or name CB )) or resid 142 or (resid 143 \ through 144 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 5 through 146 or (resid 147 and (name N or name CA or name C or name O or name C \ B )) or resid 148 through 152)) } ncs_group { reference = chain 'B' selection = (chain 'C' and resid 4 through 98) } ncs_group { reference = (chain 'E' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name SD or name CE )) or resid 2 through 259)) selection = (chain 'H' and (resid 1 through 164 or (resid 165 and (name N or name CA or name \ C or name O or name CB )) or resid 166 through 259)) } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 7 through 267) } 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: 0.010 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.890 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 40.180 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 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 : 0.003 0.049 15986 Z= 0.170 Angle : 0.661 10.568 21728 Z= 0.347 Chirality : 0.045 0.220 2651 Planarity : 0.005 0.053 2720 Dihedral : 11.671 86.190 5712 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.18 % Allowed : 6.32 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.61 (0.12), residues: 2047 helix: -5.09 (0.04), residues: 669 sheet: -2.16 (0.32), residues: 212 loop : -3.26 (0.13), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 9 HIS 0.002 0.000 HIS E 40 PHE 0.015 0.001 PHE E 184 TYR 0.011 0.001 TYR D 40 ARG 0.001 0.000 ARG H 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 504 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. REVERT: D 85 GLU cc_start: 0.7662 (pp20) cc_final: 0.7248 (pp20) REVERT: I 81 ARG cc_start: 0.7565 (ttm-80) cc_final: 0.7344 (ttm-80) REVERT: K 15 LEU cc_start: 0.7732 (mm) cc_final: 0.7187 (pp) REVERT: K 42 LEU cc_start: 0.6693 (mt) cc_final: 0.6450 (tp) REVERT: K 78 TYR cc_start: 0.6914 (m-10) cc_final: 0.6604 (m-80) REVERT: K 89 ARG cc_start: 0.6269 (mtm-85) cc_final: 0.5845 (ttt180) REVERT: L 8 ILE cc_start: 0.9144 (mm) cc_final: 0.8898 (mm) REVERT: B 51 ASP cc_start: 0.7318 (p0) cc_final: 0.7051 (m-30) REVERT: B 80 LYS cc_start: 0.7894 (tppt) cc_final: 0.7672 (mmtp) REVERT: B 82 TYR cc_start: 0.8009 (m-10) cc_final: 0.7293 (m-80) REVERT: C 80 LYS cc_start: 0.8563 (mmtp) cc_final: 0.8038 (mmtp) REVERT: F 178 ILE cc_start: 0.8325 (mm) cc_final: 0.8022 (mm) REVERT: F 252 VAL cc_start: 0.6992 (p) cc_final: 0.6782 (p) REVERT: G 99 ASP cc_start: 0.8067 (p0) cc_final: 0.7296 (p0) REVERT: G 178 ILE cc_start: 0.7701 (mm) cc_final: 0.7184 (mm) REVERT: E 203 LEU cc_start: 0.7667 (tp) cc_final: 0.7381 (tp) REVERT: H 223 ASP cc_start: 0.7632 (m-30) cc_final: 0.7429 (m-30) outliers start: 3 outliers final: 2 residues processed: 506 average time/residue: 0.3362 time to fit residues: 238.9570 Evaluate side-chains 346 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 344 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain H residue 80 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 chunk 103 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 96 optimal weight: 0.0270 chunk 118 optimal weight: 0.8980 chunk 184 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 GLN D 149 GLN K 88 GLN L 2 GLN B 22 GLN B 75 GLN F 7 ASN F 113 HIS G 105 ASN G 191 ASN G 230 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15986 Z= 0.149 Angle : 0.536 7.755 21728 Z= 0.261 Chirality : 0.040 0.169 2651 Planarity : 0.004 0.034 2720 Dihedral : 3.196 25.143 2221 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.59 % Allowed : 16.01 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.14), residues: 2047 helix: -3.20 (0.13), residues: 703 sheet: -1.63 (0.32), residues: 220 loop : -2.82 (0.15), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 177 HIS 0.002 0.000 HIS F 226 PHE 0.021 0.001 PHE L 13 TYR 0.026 0.001 TYR I 111 ARG 0.006 0.000 ARG H 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 368 time to evaluate : 1.762 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. REVERT: D 55 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7658 (mmm160) REVERT: D 85 GLU cc_start: 0.7716 (pp20) cc_final: 0.7211 (pp20) REVERT: D 129 LYS cc_start: 0.7280 (mttp) cc_final: 0.6304 (mmmt) REVERT: J 8 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7209 (mp) REVERT: J 14 LEU cc_start: 0.8308 (tp) cc_final: 0.7855 (mp) REVERT: J 55 ARG cc_start: 0.7712 (mmm-85) cc_final: 0.7339 (mmm-85) REVERT: K 15 LEU cc_start: 0.7525 (mm) cc_final: 0.7077 (pp) REVERT: K 40 TYR cc_start: 0.6819 (p90) cc_final: 0.6253 (p90) REVERT: K 78 TYR cc_start: 0.7105 (m-10) cc_final: 0.6653 (m-80) REVERT: K 138 LYS cc_start: 0.7561 (tppt) cc_final: 0.6755 (tptt) REVERT: L 8 ILE cc_start: 0.9044 (mm) cc_final: 0.8820 (mm) REVERT: B 16 LEU cc_start: 0.8468 (mt) cc_final: 0.8017 (mt) REVERT: B 71 ASN cc_start: 0.6447 (m-40) cc_final: 0.6220 (m-40) REVERT: B 75 GLN cc_start: 0.5535 (OUTLIER) cc_final: 0.5094 (mm-40) REVERT: B 86 LYS cc_start: 0.8388 (mtmm) cc_final: 0.8156 (mmtt) REVERT: F 13 ASP cc_start: 0.6846 (p0) cc_final: 0.6213 (p0) REVERT: F 66 LEU cc_start: 0.8140 (tp) cc_final: 0.7924 (tp) REVERT: F 141 MET cc_start: 0.8534 (mmm) cc_final: 0.8245 (mmm) REVERT: H 197 MET cc_start: 0.5674 (tpt) cc_final: 0.5025 (tpt) outliers start: 43 outliers final: 23 residues processed: 397 average time/residue: 0.2704 time to fit residues: 158.7407 Evaluate side-chains 360 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 335 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 43 TYR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 257 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 0.0670 chunk 57 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 184 optimal weight: 0.6980 chunk 199 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 148 optimal weight: 0.0970 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 149 GLN B 22 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 ASN F 122 HIS F 191 ASN G 7 ASN G 105 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15986 Z= 0.130 Angle : 0.503 8.884 21728 Z= 0.240 Chirality : 0.040 0.141 2651 Planarity : 0.003 0.036 2720 Dihedral : 3.045 23.577 2220 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.95 % Allowed : 17.88 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.16), residues: 2047 helix: -1.59 (0.18), residues: 705 sheet: -1.45 (0.32), residues: 226 loop : -2.54 (0.15), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 216 HIS 0.002 0.000 HIS F 226 PHE 0.025 0.001 PHE J 23 TYR 0.019 0.001 TYR I 111 ARG 0.005 0.000 ARG H 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 350 time to evaluate : 1.822 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. REVERT: D 55 ARG cc_start: 0.8052 (mmm-85) cc_final: 0.7768 (mmm160) REVERT: D 85 GLU cc_start: 0.7823 (pp20) cc_final: 0.7256 (pp20) REVERT: I 13 PHE cc_start: 0.6770 (t80) cc_final: 0.6567 (t80) REVERT: I 56 SER cc_start: 0.8566 (p) cc_final: 0.8327 (p) REVERT: J 8 ILE cc_start: 0.7768 (mt) cc_final: 0.7520 (mp) REVERT: J 14 LEU cc_start: 0.8435 (tp) cc_final: 0.7986 (mp) REVERT: K 78 TYR cc_start: 0.7065 (m-10) cc_final: 0.6710 (m-10) REVERT: K 138 LYS cc_start: 0.7537 (tppt) cc_final: 0.6730 (tptt) REVERT: L 8 ILE cc_start: 0.9036 (mm) cc_final: 0.8825 (mm) REVERT: L 101 ILE cc_start: 0.6390 (pt) cc_final: 0.6187 (pt) REVERT: B 31 MET cc_start: 0.7590 (ppp) cc_final: 0.7147 (ppp) REVERT: B 50 VAL cc_start: 0.8963 (t) cc_final: 0.8746 (m) REVERT: B 71 ASN cc_start: 0.6655 (m-40) cc_final: 0.6416 (m-40) REVERT: B 75 GLN cc_start: 0.5606 (OUTLIER) cc_final: 0.5149 (mm-40) REVERT: B 86 LYS cc_start: 0.8393 (mtmm) cc_final: 0.8130 (mmtt) REVERT: C 30 GLU cc_start: 0.7367 (mp0) cc_final: 0.7064 (mp0) REVERT: C 80 LYS cc_start: 0.8556 (mmtp) cc_final: 0.8277 (mmtp) REVERT: F 13 ASP cc_start: 0.7023 (p0) cc_final: 0.6413 (p0) REVERT: G 64 GLU cc_start: 0.4501 (tm-30) cc_final: 0.4088 (tm-30) REVERT: G 191 ASN cc_start: 0.8763 (t0) cc_final: 0.8491 (t0) REVERT: H 47 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7545 (mm-40) REVERT: H 197 MET cc_start: 0.5690 (tpt) cc_final: 0.5095 (tpt) outliers start: 49 outliers final: 30 residues processed: 379 average time/residue: 0.2818 time to fit residues: 156.5316 Evaluate side-chains 368 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 337 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain J residue 43 TYR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 235 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 0.8980 chunk 138 optimal weight: 0.0980 chunk 95 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 185 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 175 optimal weight: 4.9990 chunk 52 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN B 75 GLN F 7 ASN G 7 ASN G 105 ASN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15986 Z= 0.144 Angle : 0.515 7.911 21728 Z= 0.246 Chirality : 0.040 0.161 2651 Planarity : 0.003 0.038 2720 Dihedral : 3.007 23.492 2218 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.73 % Allowed : 18.12 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.17), residues: 2047 helix: -0.82 (0.19), residues: 725 sheet: -1.13 (0.33), residues: 224 loop : -2.31 (0.16), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 216 HIS 0.002 0.000 HIS G 113 PHE 0.025 0.001 PHE L 13 TYR 0.023 0.001 TYR I 111 ARG 0.004 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 349 time to evaluate : 1.828 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. REVERT: D 55 ARG cc_start: 0.8210 (mmm-85) cc_final: 0.8008 (mmm-85) REVERT: D 85 GLU cc_start: 0.7887 (pp20) cc_final: 0.7308 (pp20) REVERT: J 14 LEU cc_start: 0.8501 (tp) cc_final: 0.8040 (mp) REVERT: J 115 ASN cc_start: 0.5285 (m-40) cc_final: 0.4845 (p0) REVERT: K 15 LEU cc_start: 0.7091 (mt) cc_final: 0.6686 (pp) REVERT: K 78 TYR cc_start: 0.7165 (m-10) cc_final: 0.6768 (m-10) REVERT: K 138 LYS cc_start: 0.7567 (tppt) cc_final: 0.6747 (tptt) REVERT: L 67 ARG cc_start: 0.7696 (tpp-160) cc_final: 0.6681 (tpp-160) REVERT: B 31 MET cc_start: 0.7380 (ppp) cc_final: 0.6948 (ppp) REVERT: B 75 GLN cc_start: 0.5538 (OUTLIER) cc_final: 0.5106 (mt0) REVERT: B 86 LYS cc_start: 0.8443 (mtmm) cc_final: 0.8164 (mmtt) REVERT: C 8 MET cc_start: 0.7150 (mmp) cc_final: 0.6936 (mmp) REVERT: C 30 GLU cc_start: 0.7455 (mp0) cc_final: 0.7179 (mp0) REVERT: C 80 LYS cc_start: 0.8552 (mmtp) cc_final: 0.8336 (mmtp) REVERT: F 10 ASP cc_start: 0.7164 (m-30) cc_final: 0.6774 (t0) REVERT: F 13 ASP cc_start: 0.7000 (p0) cc_final: 0.6371 (p0) REVERT: G 191 ASN cc_start: 0.8796 (t0) cc_final: 0.8492 (t0) REVERT: H 47 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7777 (mm-40) REVERT: H 197 MET cc_start: 0.5771 (tpt) cc_final: 0.5067 (tpt) outliers start: 62 outliers final: 41 residues processed: 388 average time/residue: 0.2755 time to fit residues: 157.2481 Evaluate side-chains 372 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 330 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain J residue 43 TYR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 235 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 0.0770 chunk 111 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 146 optimal weight: 0.3980 chunk 80 optimal weight: 7.9990 chunk 167 optimal weight: 0.5980 chunk 135 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 7 ASN G 7 ASN ** G 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15986 Z= 0.139 Angle : 0.505 7.828 21728 Z= 0.241 Chirality : 0.040 0.142 2651 Planarity : 0.003 0.040 2720 Dihedral : 2.979 22.600 2218 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.97 % Allowed : 18.72 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.18), residues: 2047 helix: -0.32 (0.20), residues: 730 sheet: -0.88 (0.34), residues: 224 loop : -2.15 (0.16), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 177 HIS 0.002 0.000 HIS F 262 PHE 0.026 0.001 PHE L 13 TYR 0.026 0.001 TYR I 111 ARG 0.007 0.000 ARG G 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 352 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 149 GLN cc_start: 0.7490 (tm-30) cc_final: 0.7146 (tm-30) REVERT: D 85 GLU cc_start: 0.7813 (pp20) cc_final: 0.7212 (pp20) REVERT: J 12 ILE cc_start: 0.9016 (mm) cc_final: 0.8774 (mt) REVERT: J 14 LEU cc_start: 0.8554 (tp) cc_final: 0.8068 (mp) REVERT: J 38 PRO cc_start: 0.5590 (Cg_endo) cc_final: 0.5274 (Cg_exo) REVERT: J 115 ASN cc_start: 0.5339 (m-40) cc_final: 0.4920 (p0) REVERT: K 15 LEU cc_start: 0.7070 (mt) cc_final: 0.6670 (pp) REVERT: K 78 TYR cc_start: 0.7222 (m-10) cc_final: 0.6758 (m-80) REVERT: K 138 LYS cc_start: 0.7623 (tppt) cc_final: 0.6805 (tptt) REVERT: B 86 LYS cc_start: 0.8499 (mtmm) cc_final: 0.8246 (mmtt) REVERT: C 30 GLU cc_start: 0.7424 (mp0) cc_final: 0.7147 (mp0) REVERT: F 10 ASP cc_start: 0.7409 (m-30) cc_final: 0.6876 (t0) REVERT: F 13 ASP cc_start: 0.7028 (p0) cc_final: 0.6471 (p0) REVERT: F 220 ASP cc_start: 0.7001 (t0) cc_final: 0.6782 (t0) REVERT: G 130 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7504 (mt-10) REVERT: G 191 ASN cc_start: 0.8835 (t0) cc_final: 0.8555 (t0) REVERT: E 34 LYS cc_start: 0.8275 (mtpp) cc_final: 0.8053 (mtpp) REVERT: H 17 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8597 (mm) REVERT: H 47 GLN cc_start: 0.8350 (mm-40) cc_final: 0.7861 (mm-40) REVERT: H 197 MET cc_start: 0.5999 (tpt) cc_final: 0.5204 (tpt) outliers start: 66 outliers final: 47 residues processed: 395 average time/residue: 0.2685 time to fit residues: 157.0943 Evaluate side-chains 387 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 339 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain J residue 43 TYR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 136 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 80 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 115 optimal weight: 0.0870 chunk 48 optimal weight: 0.0050 chunk 196 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 overall best weight: 1.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 48 ASN F 7 ASN F 105 ASN ** G 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15986 Z= 0.296 Angle : 0.647 8.659 21728 Z= 0.317 Chirality : 0.044 0.167 2651 Planarity : 0.004 0.044 2720 Dihedral : 3.892 24.989 2218 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.64 % Allowed : 19.75 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.18), residues: 2047 helix: -0.56 (0.19), residues: 767 sheet: -1.00 (0.33), residues: 234 loop : -2.01 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 195 HIS 0.004 0.001 HIS F 262 PHE 0.032 0.002 PHE L 13 TYR 0.021 0.001 TYR I 111 ARG 0.006 0.001 ARG D 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 347 time to evaluate : 1.911 Fit side-chains TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. REVERT: A 149 GLN cc_start: 0.7504 (tm-30) cc_final: 0.7193 (tm-30) REVERT: I 7 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: I 102 ARG cc_start: 0.7496 (mtm-85) cc_final: 0.7271 (mtm-85) REVERT: J 14 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8298 (mp) REVERT: J 38 PRO cc_start: 0.5372 (Cg_endo) cc_final: 0.5156 (Cg_exo) REVERT: J 115 ASN cc_start: 0.5906 (m-40) cc_final: 0.5566 (p0) REVERT: K 15 LEU cc_start: 0.7063 (mt) cc_final: 0.6709 (pp) REVERT: B 86 LYS cc_start: 0.8649 (mtmm) cc_final: 0.8362 (mmtt) REVERT: F 7 ASN cc_start: 0.7465 (OUTLIER) cc_final: 0.7218 (p0) REVERT: F 128 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8850 (tttt) REVERT: F 185 LYS cc_start: 0.9187 (ttpp) cc_final: 0.8919 (tttt) REVERT: F 207 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7880 (pm20) REVERT: F 208 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8430 (p) REVERT: F 221 LYS cc_start: 0.8896 (ptpp) cc_final: 0.8592 (ptmt) REVERT: E 34 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7986 (mtpp) REVERT: E 87 LEU cc_start: 0.8134 (tp) cc_final: 0.7891 (tp) REVERT: E 251 PHE cc_start: 0.8442 (t80) cc_final: 0.8046 (t80) outliers start: 77 outliers final: 51 residues processed: 402 average time/residue: 0.2748 time to fit residues: 163.1000 Evaluate side-chains 386 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 329 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 43 TYR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 90 TYR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 136 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 235 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 119 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN F 7 ASN ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15986 Z= 0.177 Angle : 0.560 9.544 21728 Z= 0.269 Chirality : 0.041 0.161 2651 Planarity : 0.003 0.045 2720 Dihedral : 3.542 23.562 2218 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.55 % Allowed : 21.91 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.18), residues: 2047 helix: -0.21 (0.20), residues: 773 sheet: -0.80 (0.32), residues: 247 loop : -1.88 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 7 HIS 0.004 0.001 HIS F 262 PHE 0.028 0.001 PHE L 13 TYR 0.025 0.001 TYR I 111 ARG 0.008 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 352 time to evaluate : 1.659 Fit side-chains TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. REVERT: A 149 GLN cc_start: 0.7413 (tm-30) cc_final: 0.7105 (tm-30) REVERT: I 7 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7592 (mt-10) REVERT: J 14 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8356 (mp) REVERT: J 53 LYS cc_start: 0.8304 (pttt) cc_final: 0.7921 (ptmm) REVERT: K 7 GLU cc_start: 0.5975 (tp30) cc_final: 0.4882 (tm-30) REVERT: K 138 LYS cc_start: 0.7598 (tppt) cc_final: 0.6706 (tptt) REVERT: B 49 ARG cc_start: 0.7501 (ptt90) cc_final: 0.7143 (ptt90) REVERT: B 86 LYS cc_start: 0.8691 (mtmm) cc_final: 0.8367 (mmtt) REVERT: C 8 MET cc_start: 0.7315 (mmp) cc_final: 0.7007 (mmp) REVERT: F 7 ASN cc_start: 0.7609 (OUTLIER) cc_final: 0.7354 (p0) REVERT: F 128 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8815 (tttt) REVERT: F 185 LYS cc_start: 0.9213 (ttpp) cc_final: 0.8982 (tttt) REVERT: F 207 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7836 (pm20) REVERT: F 208 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8412 (p) REVERT: F 221 LYS cc_start: 0.8842 (ptpp) cc_final: 0.8596 (ptmt) REVERT: F 247 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7754 (mt) REVERT: G 87 MET cc_start: 0.7864 (mtm) cc_final: 0.7591 (mtm) REVERT: G 130 GLU cc_start: 0.8301 (tp30) cc_final: 0.7915 (mm-30) REVERT: E 34 LYS cc_start: 0.8224 (mtpp) cc_final: 0.7978 (mtpp) REVERT: E 189 MET cc_start: 0.7856 (ttm) cc_final: 0.7636 (ttm) REVERT: E 251 PHE cc_start: 0.8478 (t80) cc_final: 0.8206 (t80) REVERT: H 17 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8582 (mm) REVERT: H 47 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7946 (mm-40) REVERT: H 73 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7736 (mm-40) outliers start: 59 outliers final: 39 residues processed: 391 average time/residue: 0.2698 time to fit residues: 155.5140 Evaluate side-chains 381 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 334 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 43 TYR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 90 TYR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 136 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 257 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 133 optimal weight: 0.0870 chunk 96 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 153 optimal weight: 0.0970 chunk 177 optimal weight: 0.7980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 ASN B 22 GLN F 20 ASN ** G 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15986 Z= 0.145 Angle : 0.572 14.749 21728 Z= 0.269 Chirality : 0.040 0.142 2651 Planarity : 0.003 0.060 2720 Dihedral : 3.372 23.026 2218 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.13 % Allowed : 22.88 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.19), residues: 2047 helix: 0.12 (0.20), residues: 770 sheet: -0.63 (0.33), residues: 241 loop : -1.80 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 7 HIS 0.003 0.001 HIS G 62 PHE 0.030 0.001 PHE I 13 TYR 0.024 0.001 TYR I 111 ARG 0.007 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 343 time to evaluate : 1.823 Fit side-chains TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. REVERT: A 149 GLN cc_start: 0.7398 (tm-30) cc_final: 0.7092 (tm-30) REVERT: I 7 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: J 14 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8382 (mp) REVERT: J 53 LYS cc_start: 0.8213 (pttt) cc_final: 0.7819 (ptmm) REVERT: K 7 GLU cc_start: 0.6033 (tp30) cc_final: 0.4911 (tm-30) REVERT: K 129 LYS cc_start: 0.6326 (mmmt) cc_final: 0.5708 (tptt) REVERT: K 138 LYS cc_start: 0.7586 (tppt) cc_final: 0.6743 (tptt) REVERT: B 19 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7461 (mm-30) REVERT: B 49 ARG cc_start: 0.7610 (ptt90) cc_final: 0.7344 (ptt90) REVERT: B 86 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8363 (mmtt) REVERT: F 64 GLU cc_start: 0.6894 (tt0) cc_final: 0.6684 (tt0) REVERT: F 128 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8811 (tttt) REVERT: F 207 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7810 (pm20) REVERT: F 208 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8358 (p) REVERT: F 247 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7670 (mt) REVERT: G 130 GLU cc_start: 0.8330 (tp30) cc_final: 0.7947 (mm-30) REVERT: E 34 LYS cc_start: 0.8244 (mtpp) cc_final: 0.7997 (mtpp) REVERT: E 189 MET cc_start: 0.7808 (ttm) cc_final: 0.7579 (ttm) REVERT: E 251 PHE cc_start: 0.8428 (t80) cc_final: 0.8044 (t80) REVERT: H 17 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8542 (mm) REVERT: H 46 ARG cc_start: 0.8304 (tpm170) cc_final: 0.8094 (tpt170) REVERT: H 47 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7942 (mm-40) REVERT: H 73 GLN cc_start: 0.8318 (mm-40) cc_final: 0.7831 (mm-40) outliers start: 52 outliers final: 38 residues processed: 377 average time/residue: 0.2731 time to fit residues: 151.2994 Evaluate side-chains 379 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 334 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 43 TYR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 90 TYR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 136 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 257 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 0.0370 chunk 171 optimal weight: 10.0000 chunk 182 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 143 optimal weight: 0.1980 chunk 55 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN ** G 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15986 Z= 0.182 Angle : 0.586 14.022 21728 Z= 0.278 Chirality : 0.041 0.137 2651 Planarity : 0.003 0.047 2720 Dihedral : 3.441 22.841 2218 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.25 % Allowed : 23.00 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.19), residues: 2047 helix: 0.17 (0.20), residues: 779 sheet: -0.46 (0.32), residues: 251 loop : -1.71 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 7 HIS 0.003 0.001 HIS G 62 PHE 0.027 0.001 PHE I 13 TYR 0.031 0.001 TYR D 40 ARG 0.005 0.000 ARG K 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 330 time to evaluate : 1.588 Fit side-chains TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. REVERT: A 149 GLN cc_start: 0.7358 (tm-30) cc_final: 0.7043 (tm-30) REVERT: I 7 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: I 152 TYR cc_start: 0.5971 (m-80) cc_final: 0.5709 (m-80) REVERT: J 14 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8358 (mp) REVERT: J 53 LYS cc_start: 0.8168 (pttt) cc_final: 0.7846 (ptmm) REVERT: B 49 ARG cc_start: 0.7719 (ptt90) cc_final: 0.7446 (ptt90) REVERT: B 86 LYS cc_start: 0.8728 (mtmm) cc_final: 0.8396 (mmtt) REVERT: C 8 MET cc_start: 0.7295 (mmp) cc_final: 0.7042 (mmp) REVERT: F 130 GLU cc_start: 0.8147 (tp30) cc_final: 0.7863 (tp30) REVERT: F 185 LYS cc_start: 0.9196 (ttpp) cc_final: 0.8970 (tttt) REVERT: F 207 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7869 (pm20) REVERT: F 208 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8416 (p) REVERT: F 247 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7720 (mt) REVERT: G 130 GLU cc_start: 0.8291 (tp30) cc_final: 0.8000 (mm-30) REVERT: E 34 LYS cc_start: 0.8233 (mtpp) cc_final: 0.7955 (mtpp) REVERT: E 189 MET cc_start: 0.7849 (ttm) cc_final: 0.7633 (ttm) REVERT: H 17 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8532 (mm) REVERT: H 46 ARG cc_start: 0.8196 (tpm170) cc_final: 0.7904 (tpt170) REVERT: H 47 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7931 (mm-40) REVERT: H 66 ILE cc_start: 0.9051 (tp) cc_final: 0.8742 (tp) REVERT: H 73 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7754 (mm-40) outliers start: 54 outliers final: 40 residues processed: 367 average time/residue: 0.2758 time to fit residues: 149.0079 Evaluate side-chains 372 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 326 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 43 TYR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 90 TYR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 235 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 134 optimal weight: 0.3980 chunk 202 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 124 optimal weight: 0.2980 chunk 98 optimal weight: 0.9990 chunk 127 optimal weight: 0.0060 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 ASN B 22 GLN G 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15986 Z= 0.142 Angle : 0.577 13.758 21728 Z= 0.270 Chirality : 0.040 0.138 2651 Planarity : 0.003 0.049 2720 Dihedral : 3.308 22.471 2218 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.59 % Allowed : 23.96 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 2047 helix: 0.37 (0.20), residues: 778 sheet: -0.37 (0.34), residues: 236 loop : -1.66 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 29 HIS 0.002 0.000 HIS G 62 PHE 0.027 0.001 PHE I 13 TYR 0.034 0.001 TYR D 40 ARG 0.006 0.000 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 338 time to evaluate : 1.728 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. REVERT: A 149 GLN cc_start: 0.7251 (tm-30) cc_final: 0.6984 (tm-30) REVERT: D 1 MET cc_start: 0.1346 (mmt) cc_final: 0.0863 (mtt) REVERT: I 7 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: I 152 TYR cc_start: 0.5943 (m-80) cc_final: 0.5656 (m-80) REVERT: J 14 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8381 (mp) REVERT: J 53 LYS cc_start: 0.8169 (pttt) cc_final: 0.7850 (ptmm) REVERT: K 129 LYS cc_start: 0.6155 (mmmt) cc_final: 0.5689 (tptt) REVERT: B 86 LYS cc_start: 0.8697 (mtmm) cc_final: 0.8358 (mmtt) REVERT: C 8 MET cc_start: 0.7325 (mmp) cc_final: 0.7081 (mmp) REVERT: C 32 ARG cc_start: 0.7409 (ptt-90) cc_final: 0.7132 (ptt-90) REVERT: F 247 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7644 (mt) REVERT: G 130 GLU cc_start: 0.8230 (tp30) cc_final: 0.7989 (tp30) REVERT: E 34 LYS cc_start: 0.8157 (mtpp) cc_final: 0.7883 (mtpp) REVERT: H 17 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8563 (mm) REVERT: H 46 ARG cc_start: 0.8146 (tpm170) cc_final: 0.7878 (tpt170) REVERT: H 47 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7971 (mm-40) REVERT: H 66 ILE cc_start: 0.9040 (tp) cc_final: 0.8752 (tp) REVERT: H 73 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7763 (mm-40) outliers start: 43 outliers final: 35 residues processed: 367 average time/residue: 0.2747 time to fit residues: 148.6028 Evaluate side-chains 372 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 333 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 43 TYR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 90 TYR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 235 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 161 optimal weight: 0.0980 chunk 67 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 0.0970 chunk 141 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN ** G 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.167610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.130525 restraints weight = 23324.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129094 restraints weight = 17845.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130208 restraints weight = 19128.423| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15986 Z= 0.175 Angle : 0.592 13.493 21728 Z= 0.279 Chirality : 0.041 0.141 2651 Planarity : 0.003 0.062 2720 Dihedral : 3.376 21.961 2218 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.65 % Allowed : 24.14 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.19), residues: 2047 helix: 0.52 (0.20), residues: 768 sheet: -0.29 (0.33), residues: 252 loop : -1.57 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 7 HIS 0.003 0.001 HIS G 62 PHE 0.027 0.001 PHE I 13 TYR 0.034 0.001 TYR D 40 ARG 0.007 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3612.52 seconds wall clock time: 66 minutes 27.35 seconds (3987.35 seconds total)