Starting phenix.real_space_refine on Sat Aug 23 23:57:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zy2_11547/08_2025/6zy2_11547.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zy2_11547/08_2025/6zy2_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 { model { file = "/net/cci-nas-00/data/ceres_data/6zy2_11547/08_2025/6zy2_11547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zy2_11547/08_2025/6zy2_11547.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zy2_11547/08_2025/6zy2_11547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zy2_11547/08_2025/6zy2_11547.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 65 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'GLU:plan': 4, 'ASP:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1} 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: {'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1} 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: {'ARG:plan': 2, 'GLU:plan': 1, '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, 'ARG:plan': 1, 'PHE: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: {'ASP:plan': 2, 'GLU:plan': 3} 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: 4.34, per 1000 atoms: 0.28 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 - 3.00 Amino acid : True - 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: 1.13 Conformation dependent library (CDL) restraints added in 775.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.55 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: 2.33 Time building geometry restraints manager: 1.55 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: 0.00 - 2.11: 21337 2.11 - 4.23: 305 4.23 - 6.34: 58 6.34 - 8.45: 22 8.45 - 10.57: 6 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 3.040 nonbonded pdb=" O LEU E 155 " pdb=" OG1 THR E 159 " model vdw 2.312 3.040 nonbonded pdb=" O ASP B 79 " pdb=" OG1 THR B 83 " model vdw 2.338 3.040 nonbonded pdb=" O ALA E 234 " pdb=" OG1 THR E 238 " model vdw 2.342 3.040 nonbonded pdb=" OG SER F 123 " pdb=" O LEU G 265 " model vdw 2.345 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.650 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.120 ------------------------------------------------------------------------------- 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= 0.152 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG H 147 TYR 0.011 0.001 TYR D 40 PHE 0.015 0.001 PHE E 184 TRP 0.003 0.000 TRP K 9 HIS 0.002 0.000 HIS E 40 Details of bonding type rmsd covalent geometry : bond 0.00263 (15986) covalent geometry : angle 0.66091 (21728) hydrogen bonds : bond 0.35125 ( 435) hydrogen bonds : angle 10.45814 ( 1245) *********************** 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 to be fit. rotamer outliers: 3 poor density : 504 time to evaluate : 0.626 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: 0.1522 time to fit residues: 108.6387 Evaluate side-chains 346 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 344 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.0770 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.0770 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 GLN A 6 ASN D 149 GLN K 88 GLN L 2 GLN B 22 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS F 122 HIS G 7 ASN G 105 ASN G 230 GLN H 73 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.178870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.140753 restraints weight = 23129.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.140893 restraints weight = 18234.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.141904 restraints weight = 14609.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142252 restraints weight = 11094.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142389 restraints weight = 10491.598| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15986 Z= 0.126 Angle : 0.565 7.778 21728 Z= 0.279 Chirality : 0.041 0.145 2651 Planarity : 0.004 0.036 2720 Dihedral : 3.369 25.946 2221 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.71 % Allowed : 15.71 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.21 (0.14), residues: 2047 helix: -3.19 (0.13), residues: 714 sheet: -1.73 (0.32), residues: 224 loop : -2.79 (0.15), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 124 TYR 0.027 0.001 TYR I 111 PHE 0.022 0.001 PHE L 13 TRP 0.010 0.001 TRP G 216 HIS 0.002 0.001 HIS F 226 Details of bonding type rmsd covalent geometry : bond 0.00292 (15986) covalent geometry : angle 0.56523 (21728) hydrogen bonds : bond 0.03687 ( 435) hydrogen bonds : angle 4.79368 ( 1245) *********************** 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 414 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 369 time to evaluate : 0.594 Fit side-chains TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. REVERT: D 55 ARG cc_start: 0.8029 (mmm-85) cc_final: 0.7781 (mmm160) REVERT: D 85 GLU cc_start: 0.7827 (pp20) cc_final: 0.7346 (pp20) REVERT: D 129 LYS cc_start: 0.7368 (mttp) cc_final: 0.7138 (mtmt) REVERT: J 8 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7492 (mp) REVERT: J 14 LEU cc_start: 0.8395 (tp) cc_final: 0.7937 (mp) REVERT: K 15 LEU cc_start: 0.7411 (mm) cc_final: 0.7037 (pp) REVERT: K 42 LEU cc_start: 0.7214 (mt) cc_final: 0.6926 (tp) REVERT: K 138 LYS cc_start: 0.7670 (tppt) cc_final: 0.7036 (tptt) REVERT: L 8 ILE cc_start: 0.9066 (mm) cc_final: 0.8824 (mm) REVERT: L 77 THR cc_start: 0.5133 (OUTLIER) cc_final: 0.4836 (p) REVERT: B 71 ASN cc_start: 0.6665 (m-40) cc_final: 0.6376 (m-40) REVERT: B 78 ASN cc_start: 0.8049 (t0) cc_final: 0.7844 (t0) REVERT: F 66 LEU cc_start: 0.8187 (tp) cc_final: 0.7911 (tp) REVERT: G 30 THR cc_start: 0.8249 (t) cc_final: 0.8043 (t) REVERT: G 64 GLU cc_start: 0.4544 (tm-30) cc_final: 0.4187 (tm-30) REVERT: G 99 ASP cc_start: 0.8387 (p0) cc_final: 0.7719 (p0) REVERT: G 191 ASN cc_start: 0.8704 (t0) cc_final: 0.8456 (t0) REVERT: E 197 MET cc_start: 0.6744 (mpp) cc_final: 0.6488 (tpp) REVERT: E 209 PHE cc_start: 0.8189 (m-10) cc_final: 0.7863 (m-10) REVERT: H 197 MET cc_start: 0.5944 (tpt) cc_final: 0.5185 (tpt) outliers start: 45 outliers final: 27 residues processed: 396 average time/residue: 0.1318 time to fit residues: 76.8530 Evaluate side-chains 364 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 335 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 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 71 ILE 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 45 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 103 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 11 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 187 optimal weight: 0.5980 chunk 169 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 57 optimal weight: 0.0010 chunk 115 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 ASN G 105 ASN E 73 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.176709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.138769 restraints weight = 23407.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138949 restraints weight = 16734.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.139558 restraints weight = 15936.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140000 restraints weight = 12679.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.140205 restraints weight = 11796.455| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3270 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= 0.095 Angle : 0.522 9.581 21728 Z= 0.251 Chirality : 0.040 0.142 2651 Planarity : 0.003 0.035 2720 Dihedral : 3.164 22.332 2220 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.13 % Allowed : 18.06 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.07 (0.16), residues: 2047 helix: -1.61 (0.18), residues: 716 sheet: -1.50 (0.32), residues: 226 loop : -2.50 (0.16), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 97 TYR 0.019 0.001 TYR I 111 PHE 0.024 0.001 PHE J 23 TRP 0.008 0.001 TRP G 216 HIS 0.002 0.000 HIS F 226 Details of bonding type rmsd covalent geometry : bond 0.00218 (15986) covalent geometry : angle 0.52183 (21728) hydrogen bonds : bond 0.03087 ( 435) hydrogen bonds : angle 4.03701 ( 1245) *********************** 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 409 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 357 time to evaluate : 0.605 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: D 55 ARG cc_start: 0.8034 (mmm-85) cc_final: 0.7722 (mmm160) REVERT: D 85 GLU cc_start: 0.7871 (pp20) cc_final: 0.7370 (pp20) REVERT: I 56 SER cc_start: 0.8477 (p) cc_final: 0.8220 (p) REVERT: J 8 ILE cc_start: 0.7949 (mt) cc_final: 0.7743 (mp) REVERT: J 14 LEU cc_start: 0.8444 (tp) cc_final: 0.7982 (mp) REVERT: J 38 PRO cc_start: 0.5308 (Cg_endo) cc_final: 0.5040 (Cg_exo) REVERT: J 81 ARG cc_start: 0.7019 (tpp80) cc_final: 0.6626 (mtt-85) REVERT: K 42 LEU cc_start: 0.7165 (mt) cc_final: 0.6851 (tp) REVERT: K 138 LYS cc_start: 0.7682 (tppt) cc_final: 0.7107 (tptt) REVERT: L 8 ILE cc_start: 0.9044 (mm) cc_final: 0.8832 (mm) REVERT: B 16 LEU cc_start: 0.8394 (mt) cc_final: 0.7910 (mt) REVERT: B 50 VAL cc_start: 0.9238 (t) cc_final: 0.9003 (m) REVERT: F 13 ASP cc_start: 0.6756 (p0) cc_final: 0.6279 (p0) REVERT: G 99 ASP cc_start: 0.8274 (p0) cc_final: 0.7682 (p0) REVERT: G 191 ASN cc_start: 0.8694 (t0) cc_final: 0.8450 (t0) REVERT: H 43 LEU cc_start: 0.8730 (mt) cc_final: 0.8513 (mt) REVERT: H 47 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7763 (mm-40) outliers start: 52 outliers final: 30 residues processed: 390 average time/residue: 0.1283 time to fit residues: 74.1463 Evaluate side-chains 365 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 335 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 71 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 I residue 41 THR Chi-restraints excluded: chain I residue 84 LEU 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 L residue 41 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain E residue 36 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.3314 > 50: distance: 44 - 53: 26.543 distance: 53 - 54: 38.968 distance: 54 - 55: 25.636 distance: 55 - 56: 22.606 distance: 55 - 57: 46.914 distance: 57 - 58: 23.010 distance: 58 - 59: 34.725 distance: 58 - 61: 12.252 distance: 59 - 60: 51.411 distance: 59 - 62: 36.968 distance: 62 - 63: 26.949 distance: 63 - 64: 19.409 distance: 63 - 66: 37.330 distance: 64 - 65: 39.120 distance: 64 - 67: 25.515 distance: 67 - 68: 19.755 distance: 68 - 69: 21.084 distance: 68 - 71: 51.696 distance: 69 - 70: 38.422 distance: 69 - 76: 28.211 distance: 71 - 72: 43.665 distance: 72 - 73: 29.434 distance: 73 - 74: 25.899 distance: 74 - 75: 47.069 distance: 76 - 77: 22.205 distance: 77 - 78: 56.336 distance: 77 - 80: 54.216 distance: 78 - 79: 44.168 distance: 78 - 84: 31.641 distance: 80 - 81: 39.196 distance: 81 - 82: 35.007 distance: 81 - 83: 27.811 distance: 84 - 85: 42.865 distance: 85 - 86: 53.488 distance: 85 - 88: 31.394 distance: 86 - 87: 52.453 distance: 86 - 92: 32.825 distance: 87 - 105: 3.420 distance: 88 - 89: 23.090 distance: 89 - 90: 23.702 distance: 90 - 91: 50.546 distance: 92 - 93: 40.351 distance: 92 - 98: 38.965 distance: 93 - 94: 44.818 distance: 93 - 96: 51.004 distance: 94 - 95: 35.213 distance: 94 - 99: 21.849 distance: 96 - 97: 30.327 distance: 97 - 98: 17.399 distance: 99 - 100: 57.693 distance: 100 - 101: 48.728 distance: 100 - 103: 42.071 distance: 101 - 102: 39.329 distance: 101 - 105: 40.259 distance: 103 - 104: 15.718 distance: 105 - 106: 48.013 distance: 106 - 107: 10.662 distance: 106 - 109: 23.755 distance: 107 - 108: 48.741 distance: 107 - 114: 44.090 distance: 109 - 110: 23.715 distance: 110 - 111: 6.293 distance: 111 - 112: 8.150 distance: 111 - 113: 24.413 distance: 114 - 115: 19.306 distance: 115 - 116: 50.903 distance: 115 - 118: 25.244 distance: 116 - 117: 37.969 distance: 116 - 122: 34.349 distance: 118 - 119: 40.525 distance: 119 - 120: 45.008 distance: 119 - 121: 42.511