Starting phenix.real_space_refine on Mon Mar 18 13:36:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xp5_22284/03_2024/6xp5_22284.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xp5_22284/03_2024/6xp5_22284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xp5_22284/03_2024/6xp5_22284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xp5_22284/03_2024/6xp5_22284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xp5_22284/03_2024/6xp5_22284.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xp5_22284/03_2024/6xp5_22284.pdb" } resolution = 4.2 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= 0.032 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 57 5.16 5 C 13216 2.51 5 N 3743 2.21 5 O 4049 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "U GLU 17": "OE1" <-> "OE2" Residue "U GLU 58": "OE1" <-> "OE2" Residue "U GLU 119": "OE1" <-> "OE2" Residue "U GLU 135": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 29": "OE1" <-> "OE2" Residue "N ARG 239": "NH1" <-> "NH2" Residue "N GLU 255": "OE1" <-> "OE2" Residue "N ARG 277": "NH1" <-> "NH2" Residue "N PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 355": "NH1" <-> "NH2" Residue "N ARG 364": "NH1" <-> "NH2" Residue "N ARG 376": "NH1" <-> "NH2" Residue "N PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 606": "NH1" <-> "NH2" Residue "N PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 645": "OE1" <-> "OE2" Residue "N ASP 649": "OD1" <-> "OD2" Residue "N PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 745": "NH1" <-> "NH2" Residue "N ARG 754": "NH1" <-> "NH2" Residue "Q ARG 256": "NH1" <-> "NH2" Residue "Q ASP 260": "OD1" <-> "OD2" Residue "Q ARG 375": "NH1" <-> "NH2" Residue "Q TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 453": "NH1" <-> "NH2" Residue "Q TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "Z TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "H TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 97": "NH1" <-> "NH2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "H TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 67": "OD1" <-> "OD2" Residue "V GLU 97": "OE1" <-> "OE2" Residue "a ARG 138": "NH1" <-> "NH2" Residue "a GLU 146": "OE1" <-> "OE2" Residue "a PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 268": "NH1" <-> "NH2" Residue "a PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 708": "NH1" <-> "NH2" Residue "a ARG 732": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21065 Number of models: 1 Model: "" Number of chains: 15 Chain: "U" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1055 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 994 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "F" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1202 Classifications: {'peptide': 156} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 4 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 836 Classifications: {'peptide': 122} Incomplete info: {'backbone_only': 16, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain breaks: 3 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 89 Chain: "I" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 470 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 10, 'TRANS': 85} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 74 Chain: "N" Number of atoms: 4081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4081 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PTRANS': 33, 'TRANS': 510} Chain breaks: 7 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 516 Unresolved non-hydrogen dihedrals: 331 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 202 Chain: "Q" Number of atoms: 3571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3571 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 29, 'TRANS': 446} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 106 Chain: "Z" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 775 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "H" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1148 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "K" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 777 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 1255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1255 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 18, 'TRANS': 188} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 452 Unresolved non-hydrogen angles: 620 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 5, 'ASP:plan': 11, 'PHE:plan': 8, 'GLU:plan': 10, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 299 Chain: "V" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "a" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2941 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 356} Chain breaks: 8 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "b" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 105 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 Chain: "c" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1000 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 200} Link IDs: {'TRANS': 199} Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 600 Unresolved non-hydrogen dihedrals: 200 Planarities with less than four sites: {'UNK:plan-1': 200} Unresolved non-hydrogen planarities: 200 Time building chain proxies: 10.18, per 1000 atoms: 0.48 Number of scatterers: 21065 At special positions: 0 Unit cell: (189.608, 163.304, 233.448, 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 57 16.00 O 4049 8.00 N 3743 7.00 C 13216 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: 8.17 Conformation dependent library (CDL) restraints added in 3.7 seconds 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 17 sheets defined 49.1% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'U' and resid 3 through 29 removed outlier: 4.008A pdb=" N LEU U 16 " --> pdb=" O MET U 12 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU U 17 " --> pdb=" O ASP U 13 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP U 25 " --> pdb=" O SER U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 60 removed outlier: 3.987A pdb=" N GLU U 59 " --> pdb=" O SER U 56 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR U 60 " --> pdb=" O PRO U 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 56 through 60' Processing helix chain 'U' and resid 62 through 67 Processing helix chain 'U' and resid 67 through 77 removed outlier: 4.690A pdb=" N VAL U 73 " --> pdb=" O ARG U 69 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS U 74 " --> pdb=" O ASP U 70 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 84 removed outlier: 4.303A pdb=" N LEU U 81 " --> pdb=" O GLN U 77 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE U 82 " --> pdb=" O ILE U 78 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER U 83 " --> pdb=" O GLU U 79 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR U 84 " --> pdb=" O TYR U 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 77 through 84' Processing helix chain 'U' and resid 92 through 134 removed outlier: 3.848A pdb=" N ILE U 96 " --> pdb=" O GLU U 92 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU U 101 " --> pdb=" O GLN U 97 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU U 102 " --> pdb=" O LEU U 98 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU U 103 " --> pdb=" O LEU U 99 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP U 104 " --> pdb=" O ARG U 100 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL U 107 " --> pdb=" O GLU U 103 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN U 112 " --> pdb=" O THR U 108 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG U 113 " --> pdb=" O ALA U 109 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU U 117 " --> pdb=" O ARG U 113 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS U 118 " --> pdb=" O GLN U 114 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU U 124 " --> pdb=" O ARG U 120 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU U 127 " --> pdb=" O VAL U 123 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA U 129 " --> pdb=" O GLY U 125 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU U 130 " --> pdb=" O LYS U 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 26 removed outlier: 3.867A pdb=" N GLU D 13 " --> pdb=" O PHE D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 72 removed outlier: 5.437A pdb=" N GLU D 42 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 86 removed outlier: 3.787A pdb=" N SER D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 117 removed outlier: 3.697A pdb=" N LEU D 109 " --> pdb=" O THR D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 120 No H-bonds generated for 'chain 'D' and resid 118 through 120' Processing helix chain 'F' and resid 35 through 40 Processing helix chain 'F' and resid 48 through 54 Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 63 through 68 Processing helix chain 'F' and resid 129 through 132 removed outlier: 3.618A pdb=" N ASN F 132 " --> pdb=" O VAL F 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 129 through 132' Processing helix chain 'F' and resid 139 through 144 Processing helix chain 'F' and resid 144 through 154 removed outlier: 4.235A pdb=" N ALA F 151 " --> pdb=" O ARG F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 199 removed outlier: 3.640A pdb=" N LEU F 197 " --> pdb=" O PRO F 194 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU F 198 " --> pdb=" O ARG F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 206 removed outlier: 3.925A pdb=" N GLU F 205 " --> pdb=" O LEU F 201 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE F 206 " --> pdb=" O MET F 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 37 removed outlier: 3.910A pdb=" N GLN G 36 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 122 removed outlier: 3.558A pdb=" N ALA G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 139 Processing helix chain 'G' and resid 140 through 157 removed outlier: 4.857A pdb=" N ILE G 150 " --> pdb=" O LYS G 146 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS G 151 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR G 152 " --> pdb=" O GLN G 148 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE G 153 " --> pdb=" O ASP G 149 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE G 157 " --> pdb=" O ILE G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 195 removed outlier: 3.661A pdb=" N ARG G 193 " --> pdb=" O ASP G 189 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE G 195 " --> pdb=" O ALA G 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 66 Proline residue: I 47 - end of helix Proline residue: I 52 - end of helix Processing helix chain 'I' and resid 74 through 104 Proline residue: I 87 - end of helix Proline residue: I 92 - end of helix Processing helix chain 'N' and resid 94 through 107 removed outlier: 4.040A pdb=" N GLU N 98 " --> pdb=" O HIS N 94 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR N 102 " --> pdb=" O GLU N 98 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET N 103 " --> pdb=" O GLU N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 116 through 122 removed outlier: 4.480A pdb=" N HIS N 120 " --> pdb=" O GLY N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 235 through 257 removed outlier: 4.001A pdb=" N ARG N 239 " --> pdb=" O GLU N 235 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG N 251 " --> pdb=" O ALA N 247 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU N 252 " --> pdb=" O LEU N 248 " (cutoff:3.500A) Processing helix chain 'N' and resid 312 through 328 removed outlier: 4.231A pdb=" N ALA N 316 " --> pdb=" O GLU N 312 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL N 317 " --> pdb=" O LEU N 313 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N TRP N 320 " --> pdb=" O ALA N 316 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU N 323 " --> pdb=" O TYR N 319 " (cutoff:3.500A) Processing helix chain 'N' and resid 331 through 351 Processing helix chain 'N' and resid 352 through 359 Processing helix chain 'N' and resid 360 through 362 No H-bonds generated for 'chain 'N' and resid 360 through 362' Processing helix chain 'N' and resid 443 through 462 Processing helix chain 'N' and resid 537 through 557 removed outlier: 4.166A pdb=" N GLU N 541 " --> pdb=" O SER N 537 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA N 554 " --> pdb=" O SER N 550 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN N 555 " --> pdb=" O VAL N 551 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY N 556 " --> pdb=" O LEU N 552 " (cutoff:3.500A) Processing helix chain 'N' and resid 574 through 578 removed outlier: 3.701A pdb=" N VAL N 577 " --> pdb=" O ARG N 574 " (cutoff:3.500A) Processing helix chain 'N' and resid 652 through 669 removed outlier: 3.905A pdb=" N LEU N 662 " --> pdb=" O HIS N 658 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN N 668 " --> pdb=" O ALA N 664 " (cutoff:3.500A) Processing helix chain 'N' and resid 681 through 686 Processing helix chain 'N' and resid 687 through 689 No H-bonds generated for 'chain 'N' and resid 687 through 689' Processing helix chain 'Q' and resid 34 through 45 removed outlier: 5.576A pdb=" N ASN Q 42 " --> pdb=" O GLU Q 38 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY Q 43 " --> pdb=" O GLU Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 66 Proline residue: Q 63 - end of helix Processing helix chain 'Q' and resid 79 through 81 No H-bonds generated for 'chain 'Q' and resid 79 through 81' Processing helix chain 'Q' and resid 82 through 87 removed outlier: 4.120A pdb=" N ARG Q 86 " --> pdb=" O HIS Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 103 removed outlier: 4.243A pdb=" N PHE Q 101 " --> pdb=" O TYR Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 183 removed outlier: 3.721A pdb=" N LYS Q 174 " --> pdb=" O LEU Q 170 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG Q 175 " --> pdb=" O ALA Q 171 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA Q 181 " --> pdb=" O GLN Q 177 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 197 removed outlier: 3.601A pdb=" N GLY Q 197 " --> pdb=" O VAL Q 193 " (cutoff:3.500A) Processing helix chain 'Q' and resid 279 through 304 removed outlier: 3.705A pdb=" N ASN Q 300 " --> pdb=" O TRP Q 296 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG Q 301 " --> pdb=" O HIS Q 297 " (cutoff:3.500A) Processing helix chain 'Q' and resid 349 through 353 removed outlier: 4.000A pdb=" N MET Q 353 " --> pdb=" O GLN Q 350 " (cutoff:3.500A) Processing helix chain 'Q' and resid 354 through 369 Processing helix chain 'Q' and resid 370 through 372 No H-bonds generated for 'chain 'Q' and resid 370 through 372' Processing helix chain 'Q' and resid 373 through 378 Processing helix chain 'Q' and resid 391 through 415 removed outlier: 4.108A pdb=" N LEU Q 395 " --> pdb=" O ILE Q 391 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR Q 398 " --> pdb=" O PRO Q 394 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS Q 399 " --> pdb=" O LEU Q 395 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN Q 406 " --> pdb=" O ASN Q 402 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR Q 407 " --> pdb=" O GLN Q 403 " (cutoff:3.500A) Processing helix chain 'Q' and resid 512 through 532 Proline residue: Q 525 - end of helix removed outlier: 3.783A pdb=" N LEU Q 528 " --> pdb=" O ILE Q 524 " (cutoff:3.500A) Processing helix chain 'Q' and resid 617 through 622 Processing helix chain 'Z' and resid 28 through 37 removed outlier: 3.866A pdb=" N PHE Z 35 " --> pdb=" O LEU Z 31 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL Z 36 " --> pdb=" O GLU Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 51 Processing helix chain 'Z' and resid 52 through 55 Processing helix chain 'Z' and resid 56 through 64 Processing helix chain 'Z' and resid 85 through 93 removed outlier: 3.680A pdb=" N GLN Z 89 " --> pdb=" O LEU Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 95 through 102 removed outlier: 4.000A pdb=" N VAL Z 102 " --> pdb=" O GLN Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 102 through 110 removed outlier: 3.695A pdb=" N ARG Z 110 " --> pdb=" O ALA Z 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 9 No H-bonds generated for 'chain 'H' and resid 7 through 9' Processing helix chain 'H' and resid 10 through 38 removed outlier: 3.684A pdb=" N ILE H 36 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR H 38 " --> pdb=" O ASN H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 67 removed outlier: 3.582A pdb=" N ASN H 57 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR H 66 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU H 67 " --> pdb=" O GLU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 75 Processing helix chain 'H' and resid 82 through 87 removed outlier: 3.934A pdb=" N ARG H 86 " --> pdb=" O ASN H 82 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR H 87 " --> pdb=" O PHE H 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 82 through 87' Processing helix chain 'H' and resid 90 through 96 removed outlier: 4.377A pdb=" N GLN H 94 " --> pdb=" O HIS H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 107 Processing helix chain 'H' and resid 165 through 181 Processing helix chain 'H' and resid 184 through 189 removed outlier: 3.833A pdb=" N TYR H 187 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR H 188 " --> pdb=" O LYS H 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 57 removed outlier: 3.771A pdb=" N ILE K 31 " --> pdb=" O PRO K 27 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLN K 32 " --> pdb=" O ALA K 28 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU K 34 " --> pdb=" O ARG K 30 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP K 38 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ASN K 39 " --> pdb=" O GLY K 35 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP K 40 " --> pdb=" O GLU K 36 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU K 45 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN K 46 " --> pdb=" O ALA K 42 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA K 50 " --> pdb=" O GLN K 46 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALA K 51 " --> pdb=" O HIS K 47 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU K 52 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR K 57 " --> pdb=" O LYS K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 123 Processing helix chain 'K' and resid 141 through 148 Processing helix chain 'K' and resid 148 through 153 Processing helix chain 'R' and resid 19 through 27 Processing helix chain 'R' and resid 101 through 106 Processing helix chain 'R' and resid 145 through 154 Processing helix chain 'R' and resid 219 through 237 Processing helix chain 'V' and resid 16 through 29 removed outlier: 3.824A pdb=" N ALA V 20 " --> pdb=" O ASN V 16 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR V 24 " --> pdb=" O ALA V 20 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP V 28 " --> pdb=" O THR V 24 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 32 No H-bonds generated for 'chain 'V' and resid 30 through 32' Processing helix chain 'V' and resid 33 through 38 removed outlier: 3.567A pdb=" N ILE V 37 " --> pdb=" O ALA V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 62 removed outlier: 4.657A pdb=" N MET V 52 " --> pdb=" O GLY V 48 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA V 53 " --> pdb=" O TYR V 49 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU V 54 " --> pdb=" O SER V 50 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N HIS V 59 " --> pdb=" O SER V 55 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 73 removed outlier: 4.849A pdb=" N SER V 70 " --> pdb=" O GLU V 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 90 through 119 removed outlier: 4.329A pdb=" N GLN V 94 " --> pdb=" O GLU V 90 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU V 97 " --> pdb=" O ALA V 93 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL V 106 " --> pdb=" O ASP V 102 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N TRP V 107 " --> pdb=" O ALA V 103 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP V 108 " --> pdb=" O GLU V 104 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP V 115 " --> pdb=" O ASN V 111 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG V 116 " --> pdb=" O GLU V 112 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU V 117 " --> pdb=" O MET V 113 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU V 119 " --> pdb=" O ASP V 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 128 removed outlier: 4.119A pdb=" N LYS a 128 " --> pdb=" O LEU a 124 " (cutoff:3.500A) Processing helix chain 'a' and resid 193 through 197 Processing helix chain 'a' and resid 200 through 205 Processing helix chain 'a' and resid 206 through 208 No H-bonds generated for 'chain 'a' and resid 206 through 208' Processing helix chain 'a' and resid 221 through 236 removed outlier: 3.876A pdb=" N ARG a 230 " --> pdb=" O ALA a 226 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU a 231 " --> pdb=" O ASN a 227 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA a 232 " --> pdb=" O PHE a 228 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL a 233 " --> pdb=" O GLU a 229 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU a 234 " --> pdb=" O ARG a 230 " (cutoff:3.500A) Processing helix chain 'a' and resid 252 through 266 removed outlier: 4.637A pdb=" N ARG a 258 " --> pdb=" O GLU a 254 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU a 259 " --> pdb=" O SER a 255 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU a 264 " --> pdb=" O HIS a 260 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN a 265 " --> pdb=" O ALA a 261 " (cutoff:3.500A) Processing helix chain 'a' and resid 276 through 281 Processing helix chain 'a' and resid 282 through 284 No H-bonds generated for 'chain 'a' and resid 282 through 284' Processing helix chain 'a' and resid 713 through 717 removed outlier: 3.720A pdb=" N ARG a 716 " --> pdb=" O ASP a 713 " (cutoff:3.500A) Processing helix chain 'a' and resid 719 through 725 removed outlier: 3.511A pdb=" N ASP a 723 " --> pdb=" O GLU a 719 " (cutoff:3.500A) Processing helix chain 'b' and resid 474 through 493 removed outlier: 4.302A pdb=" N UNK b 478 " --> pdb=" O UNK b 474 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N UNK b 479 " --> pdb=" O UNK b 475 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N UNK b 483 " --> pdb=" O UNK b 479 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N UNK b 493 " --> pdb=" O UNK b 489 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 24 Processing helix chain 'c' and resid 28 through 41 removed outlier: 4.413A pdb=" N UNK c 32 " --> pdb=" O UNK c 28 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N UNK c 34 " --> pdb=" O UNK c 30 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 67 Processing helix chain 'c' and resid 79 through 100 removed outlier: 4.035A pdb=" N UNK c 87 " --> pdb=" O UNK c 83 " (cutoff:3.500A) Processing helix chain 'c' and resid 106 through 115 Processing helix chain 'c' and resid 116 through 119 Processing helix chain 'c' and resid 130 through 140 removed outlier: 3.763A pdb=" N UNK c 134 " --> pdb=" O UNK c 130 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N UNK c 140 " --> pdb=" O UNK c 136 " (cutoff:3.500A) Processing helix chain 'c' and resid 143 through 156 Processing helix chain 'c' and resid 173 through 186 removed outlier: 3.740A pdb=" N UNK c 177 " --> pdb=" O UNK c 173 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N UNK c 178 " --> pdb=" O UNK c 174 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N UNK c 182 " --> pdb=" O UNK c 178 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N UNK c 183 " --> pdb=" O UNK c 179 " (cutoff:3.500A) Processing helix chain 'c' and resid 192 through 204 Processing sheet with id=AA1, first strand: chain 'F' and resid 82 through 84 removed outlier: 3.986A pdb=" N GLY F 124 " --> pdb=" O LYS F 107 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR F 109 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL F 122 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 274 through 277 removed outlier: 4.122A pdb=" N GLU N 283 " --> pdb=" O PHE N 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 369 through 370 removed outlier: 3.944A pdb=" N LEU N 369 " --> pdb=" O HIS N 381 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE N 380 " --> pdb=" O LYS N 393 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 492 through 493 removed outlier: 3.987A pdb=" N ASP N 512 " --> pdb=" O ASN N 507 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 584 through 585 removed outlier: 3.716A pdb=" N SER N 584 " --> pdb=" O TRP N 598 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP N 598 " --> pdb=" O SER N 584 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 706 through 707 removed outlier: 3.953A pdb=" N TRP N 706 " --> pdb=" O THR N 755 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR N 755 " --> pdb=" O TRP N 706 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'Q' and resid 199 through 202 removed outlier: 4.694A pdb=" N GLN Q 199 " --> pdb=" O LYS Q 213 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 250 through 252 removed outlier: 3.532A pdb=" N SER Q 250 " --> pdb=" O ALA Q 333 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE Q 318 " --> pdb=" O ILE Q 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Q' and resid 427 through 428 Processing sheet with id=AB1, first strand: chain 'Q' and resid 461 through 462 removed outlier: 3.567A pdb=" N THR Q 462 " --> pdb=" O ARG Q 470 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG Q 470 " --> pdb=" O THR Q 462 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'Q' and resid 596 through 599 Processing sheet with id=AB3, first strand: chain 'R' and resid 8 through 9 removed outlier: 3.753A pdb=" N GLY R 9 " --> pdb=" O TRP R 208 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP R 208 " --> pdb=" O GLY R 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 61 through 63 Processing sheet with id=AB5, first strand: chain 'a' and resid 161 through 162 removed outlier: 3.682A pdb=" N VAL a 179 " --> pdb=" O LEU a 171 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'a' and resid 287 through 289 Processing sheet with id=AB7, first strand: chain 'a' and resid 381 through 386 removed outlier: 6.674A pdb=" N ARG a 706 " --> pdb=" O GLU a 382 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'a' and resid 582 through 585 removed outlier: 3.755A pdb=" N SER a 585 " --> pdb=" O MET a 690 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL a 693 " --> pdb=" O LYS a 661 " (cutoff:3.500A) 839 hydrogen bonds defined for protein. 2436 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: 5.93 Time building geometry restraints manager: 8.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6975 1.34 - 1.45: 2375 1.45 - 1.57: 11926 1.57 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 21381 Sorted by residual: bond pdb=" CA ILE N 785 " pdb=" CB ILE N 785 " ideal model delta sigma weight residual 1.553 1.533 0.020 7.40e-03 1.83e+04 7.21e+00 bond pdb=" CG LEU N 252 " pdb=" CD1 LEU N 252 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.00e+00 bond pdb=" C LEU H 100 " pdb=" N GLU H 101 " ideal model delta sigma weight residual 1.329 1.297 0.032 1.86e-02 2.89e+03 2.88e+00 bond pdb=" C GLY U 36 " pdb=" N PRO U 37 " ideal model delta sigma weight residual 1.330 1.350 -0.020 1.25e-02 6.40e+03 2.56e+00 bond pdb=" N PHE N 299 " pdb=" CA PHE N 299 " ideal model delta sigma weight residual 1.457 1.478 -0.020 1.29e-02 6.01e+03 2.48e+00 ... (remaining 21376 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.14: 525 106.14 - 113.14: 11699 113.14 - 120.13: 7305 120.13 - 127.13: 9261 127.13 - 134.13: 232 Bond angle restraints: 29022 Sorted by residual: angle pdb=" N PRO N 678 " pdb=" CA PRO N 678 " pdb=" CB PRO N 678 " ideal model delta sigma weight residual 103.25 113.49 -10.24 1.05e+00 9.07e-01 9.52e+01 angle pdb=" N PRO N 230 " pdb=" CA PRO N 230 " pdb=" CB PRO N 230 " ideal model delta sigma weight residual 103.08 110.89 -7.81 9.70e-01 1.06e+00 6.48e+01 angle pdb=" N PRO N 231 " pdb=" CA PRO N 231 " pdb=" CB PRO N 231 " ideal model delta sigma weight residual 103.25 111.34 -8.09 1.05e+00 9.07e-01 5.94e+01 angle pdb=" N PRO N 789 " pdb=" CA PRO N 789 " pdb=" CB PRO N 789 " ideal model delta sigma weight residual 103.25 111.28 -8.03 1.05e+00 9.07e-01 5.85e+01 angle pdb=" N PRO N 779 " pdb=" CA PRO N 779 " pdb=" CB PRO N 779 " ideal model delta sigma weight residual 103.25 111.12 -7.87 1.05e+00 9.07e-01 5.61e+01 ... (remaining 29017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 11684 17.72 - 35.45: 1076 35.45 - 53.17: 172 53.17 - 70.89: 24 70.89 - 88.62: 20 Dihedral angle restraints: 12976 sinusoidal: 4490 harmonic: 8486 Sorted by residual: dihedral pdb=" CA LEU N 497 " pdb=" C LEU N 497 " pdb=" N ASP N 498 " pdb=" CA ASP N 498 " ideal model delta harmonic sigma weight residual 180.00 132.35 47.65 0 5.00e+00 4.00e-02 9.08e+01 dihedral pdb=" CA SER N 435 " pdb=" C SER N 435 " pdb=" N GLN N 436 " pdb=" CA GLN N 436 " ideal model delta harmonic sigma weight residual -180.00 -142.16 -37.84 0 5.00e+00 4.00e-02 5.73e+01 dihedral pdb=" CA LEU K 154 " pdb=" C LEU K 154 " pdb=" N PRO K 155 " pdb=" CA PRO K 155 " ideal model delta harmonic sigma weight residual 180.00 144.41 35.59 0 5.00e+00 4.00e-02 5.07e+01 ... (remaining 12973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2908 0.065 - 0.130: 418 0.130 - 0.196: 32 0.196 - 0.261: 33 0.261 - 0.326: 3 Chirality restraints: 3394 Sorted by residual: chirality pdb=" CB THR Q 464 " pdb=" CA THR Q 464 " pdb=" OG1 THR Q 464 " pdb=" CG2 THR Q 464 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA PRO K 24 " pdb=" N PRO K 24 " pdb=" C PRO K 24 " pdb=" CB PRO K 24 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA PRO N 108 " pdb=" N PRO N 108 " pdb=" C PRO N 108 " pdb=" CB PRO N 108 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 3391 not shown) Planarity restraints: 3801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY U 36 " 0.052 5.00e-02 4.00e+02 7.83e-02 9.80e+00 pdb=" N PRO U 37 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO U 37 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO U 37 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 47 " -0.013 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C LEU D 47 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU D 47 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS D 48 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 206 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO Q 207 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO Q 207 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO Q 207 " -0.033 5.00e-02 4.00e+02 ... (remaining 3798 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 661 2.68 - 3.24: 23126 3.24 - 3.79: 30900 3.79 - 4.35: 37870 4.35 - 4.90: 57495 Nonbonded interactions: 150052 Sorted by model distance: nonbonded pdb=" OG1 THR N 268 " pdb=" OG1 THR N 275 " model vdw 2.131 2.440 nonbonded pdb=" OH TYR V 26 " pdb=" O LYS V 63 " model vdw 2.135 2.440 nonbonded pdb=" OG SER Q 417 " pdb=" O ARG Q 420 " model vdw 2.159 2.440 nonbonded pdb=" OE2 GLU Q 206 " pdb=" OG1 THR Q 209 " model vdw 2.182 2.440 nonbonded pdb=" O TRP a 324 " pdb=" ND2 ASN a 328 " model vdw 2.185 2.520 ... (remaining 150047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.460 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: 24.400 Check model and map are aligned: 0.350 Set scattering table: 0.200 Process input model: 51.520 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21381 Z= 0.249 Angle : 0.897 10.522 29022 Z= 0.541 Chirality : 0.051 0.326 3394 Planarity : 0.005 0.078 3801 Dihedral : 14.323 88.618 7414 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.92 % Allowed : 15.88 % Favored : 83.20 % Rotamer: Outliers : 0.27 % Allowed : 7.32 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.33 % Twisted General : 0.36 % 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: -5.23 (0.13), residues: 2607 helix: -2.19 (0.14), residues: 1024 sheet: -3.85 (0.24), residues: 295 loop : -4.61 (0.14), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP a 378 HIS 0.008 0.001 HIS U 30 PHE 0.016 0.002 PHE U 19 TYR 0.013 0.001 TYR F 44 ARG 0.009 0.001 ARG U 113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 292 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable