Starting phenix.real_space_refine on Sat Jan 20 18:10:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch9_30372/01_2024/7ch9_30372_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch9_30372/01_2024/7ch9_30372.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch9_30372/01_2024/7ch9_30372_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch9_30372/01_2024/7ch9_30372_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch9_30372/01_2024/7ch9_30372_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch9_30372/01_2024/7ch9_30372.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch9_30372/01_2024/7ch9_30372.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch9_30372/01_2024/7ch9_30372_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch9_30372/01_2024/7ch9_30372_updated.pdb" } resolution = 3.5 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= -0.005 sd= 1.035 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 44 5.16 5 C 10271 2.51 5 N 2669 2.21 5 O 2991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 4": "NH1" <-> "NH2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "D PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "G ARG 9": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ARG 15": "NH1" <-> "NH2" Residue "G ARG 26": "NH1" <-> "NH2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 88": "OE1" <-> "OE2" Residue "G ARG 101": "NH1" <-> "NH2" Residue "G ARG 115": "NH1" <-> "NH2" Residue "G GLU 131": "OE1" <-> "OE2" Residue "G GLU 137": "OE1" <-> "OE2" Residue "G PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 237": "NH1" <-> "NH2" Residue "G ARG 241": "NH1" <-> "NH2" Residue "H ARG 9": "NH1" <-> "NH2" Residue "H ARG 11": "NH1" <-> "NH2" Residue "H ARG 15": "NH1" <-> "NH2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 39": "NH1" <-> "NH2" Residue "H ARG 115": "NH1" <-> "NH2" Residue "H PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 237": "NH1" <-> "NH2" Residue "H ARG 241": "NH1" <-> "NH2" Residue "I ARG 18": "NH1" <-> "NH2" Residue "I ARG 33": "NH1" <-> "NH2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I ARG 77": "NH1" <-> "NH2" Residue "I ARG 84": "NH1" <-> "NH2" Residue "I GLU 118": "OE1" <-> "OE2" Residue "I ARG 135": "NH1" <-> "NH2" Residue "I ARG 151": "NH1" <-> "NH2" Residue "I ARG 152": "NH1" <-> "NH2" Residue "I ARG 185": "NH1" <-> "NH2" Residue "I GLU 207": "OE1" <-> "OE2" Residue "I ARG 222": "NH1" <-> "NH2" Residue "I ARG 239": "NH1" <-> "NH2" Residue "I ARG 259": "NH1" <-> "NH2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ARG 33": "NH1" <-> "NH2" Residue "J ARG 59": "NH1" <-> "NH2" Residue "J ARG 77": "NH1" <-> "NH2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J ARG 151": "NH1" <-> "NH2" Residue "J ARG 152": "NH1" <-> "NH2" Residue "J ARG 185": "NH1" <-> "NH2" Residue "J ARG 222": "NH1" <-> "NH2" Residue "J ARG 239": "NH1" <-> "NH2" Residue "J ARG 259": "NH1" <-> "NH2" Residue "K ARG 7": "NH1" <-> "NH2" Residue "K GLU 8": "OE1" <-> "OE2" Residue "K GLU 13": "OE1" <-> "OE2" Residue "K ARG 29": "NH1" <-> "NH2" Residue "K GLU 52": "OE1" <-> "OE2" Residue "K ARG 67": "NH1" <-> "NH2" Residue "K ARG 70": "NH1" <-> "NH2" Residue "K ARG 79": "NH1" <-> "NH2" Residue "L ARG 7": "NH1" <-> "NH2" Residue "L ARG 29": "NH1" <-> "NH2" Residue "L GLU 43": "OE1" <-> "OE2" Residue "L GLU 52": "OE1" <-> "OE2" Residue "L ARG 67": "NH1" <-> "NH2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "L ARG 79": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 15978 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1088 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 148} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1068 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 146} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1079 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 146} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1083 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 146} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1090 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 147} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1070 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 146} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1928 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 250} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1908 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 250} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "I" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2015 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 245} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 1991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1991 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 245} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'TYR:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "K" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 721 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "L" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 721 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'LPP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'LPP:plan-2': 1, 'LPP:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'LPP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'LPP:plan-2': 2, 'LPP:plan-1': 2} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'LPP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'LPP:plan-2': 2, 'LPP:plan-1': 2} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'LPP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'LPP:plan-2': 1, 'LPP:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'LPP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'LPP:plan-2': 1, 'LPP:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {'LPP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'LPP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.68, per 1000 atoms: 0.54 Number of scatterers: 15978 At special positions: 0 Unit cell: (101, 121, 146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 3 15.00 O 2991 8.00 N 2669 7.00 C 10271 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: 6.12 Conformation dependent library (CDL) restraints added in 2.8 seconds 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3784 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 21 sheets defined 40.0% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 3 through 19 Processing helix chain 'A' and resid 138 through 144 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 139 through 142 No H-bonds generated for 'chain 'B' and resid 139 through 142' Processing helix chain 'C' and resid 7 through 28 removed outlier: 4.763A pdb=" N VAL C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 144 Processing helix chain 'D' and resid 4 through 26 removed outlier: 3.794A pdb=" N ILE D 8 " --> pdb=" O ARG D 4 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLY D 9 " --> pdb=" O THR D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 142 Processing helix chain 'E' and resid 3 through 19 removed outlier: 3.702A pdb=" N GLY E 17 " --> pdb=" O PHE E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 144 Processing helix chain 'E' and resid 146 through 149 No H-bonds generated for 'chain 'E' and resid 146 through 149' Processing helix chain 'F' and resid 5 through 25 removed outlier: 3.631A pdb=" N ILE F 8 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F 10 " --> pdb=" O GLU F 7 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA F 16 " --> pdb=" O PHE F 13 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA F 20 " --> pdb=" O GLY F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 143 No H-bonds generated for 'chain 'F' and resid 140 through 143' Processing helix chain 'G' and resid 6 through 36 removed outlier: 3.527A pdb=" N VAL G 21 " --> pdb=" O GLY G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 55 Processing helix chain 'G' and resid 57 through 83 removed outlier: 4.271A pdb=" N ALA G 61 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE G 62 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL G 65 " --> pdb=" O ILE G 62 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE G 70 " --> pdb=" O GLY G 67 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL G 73 " --> pdb=" O ILE G 70 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA G 75 " --> pdb=" O MET G 72 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR G 79 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU G 82 " --> pdb=" O TYR G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 101 removed outlier: 4.978A pdb=" N GLY G 92 " --> pdb=" O GLN G 89 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL G 95 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA G 96 " --> pdb=" O GLN G 93 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR G 98 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU G 99 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU G 100 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG G 101 " --> pdb=" O THR G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 115 removed outlier: 3.766A pdb=" N GLY G 114 " --> pdb=" O LEU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 130 Processing helix chain 'G' and resid 135 through 139 Processing helix chain 'G' and resid 144 through 147 No H-bonds generated for 'chain 'G' and resid 144 through 147' Processing helix chain 'G' and resid 149 through 178 removed outlier: 3.678A pdb=" N ILE G 157 " --> pdb=" O TRP G 153 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER G 158 " --> pdb=" O ALA G 154 " (cutoff:3.500A) Proline residue: G 160 - end of helix removed outlier: 3.778A pdb=" N VAL G 177 " --> pdb=" O GLY G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 195 Processing helix chain 'G' and resid 199 through 220 removed outlier: 5.442A pdb=" N LEU G 204 " --> pdb=" O THR G 200 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASN G 205 " --> pdb=" O GLU G 201 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE G 213 " --> pdb=" O LYS G 209 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE G 220 " --> pdb=" O VAL G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 226 No H-bonds generated for 'chain 'G' and resid 223 through 226' Processing helix chain 'G' and resid 232 through 259 removed outlier: 3.798A pdb=" N SER G 236 " --> pdb=" O SER G 232 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR G 240 " --> pdb=" O SER G 236 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL G 243 " --> pdb=" O THR G 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 36 removed outlier: 3.847A pdb=" N GLY H 25 " --> pdb=" O VAL H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 55 Processing helix chain 'H' and resid 57 through 82 removed outlier: 3.616A pdb=" N LEU H 60 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA H 61 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE H 62 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL H 64 " --> pdb=" O ALA H 61 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL H 65 " --> pdb=" O ILE H 62 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE H 70 " --> pdb=" O GLY H 67 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA H 75 " --> pdb=" O MET H 72 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN H 77 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TYR H 79 " --> pdb=" O LEU H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 95 No H-bonds generated for 'chain 'H' and resid 92 through 95' Processing helix chain 'H' and resid 98 through 101 No H-bonds generated for 'chain 'H' and resid 98 through 101' Processing helix chain 'H' and resid 103 through 115 removed outlier: 4.052A pdb=" N GLY H 114 " --> pdb=" O LEU H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 129 removed outlier: 3.656A pdb=" N MET H 127 " --> pdb=" O GLU H 123 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS H 128 " --> pdb=" O ILE H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 137 No H-bonds generated for 'chain 'H' and resid 134 through 137' Processing helix chain 'H' and resid 143 through 147 Processing helix chain 'H' and resid 149 through 179 removed outlier: 3.513A pdb=" N ILE H 157 " --> pdb=" O TRP H 153 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER H 158 " --> pdb=" O ALA H 154 " (cutoff:3.500A) Proline residue: H 160 - end of helix Processing helix chain 'H' and resid 186 through 195 Processing helix chain 'H' and resid 199 through 215 removed outlier: 5.230A pdb=" N LEU H 204 " --> pdb=" O THR H 200 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN H 205 " --> pdb=" O GLU H 201 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE H 213 " --> pdb=" O LYS H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 226 removed outlier: 3.846A pdb=" N GLY H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 260 removed outlier: 4.096A pdb=" N THR H 240 " --> pdb=" O SER H 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 54 removed outlier: 3.736A pdb=" N ILE I 54 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 86 removed outlier: 4.414A pdb=" N ASP I 82 " --> pdb=" O GLY I 78 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS I 85 " --> pdb=" O PHE I 81 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN I 86 " --> pdb=" O ASP I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 107 Processing helix chain 'I' and resid 110 through 113 No H-bonds generated for 'chain 'I' and resid 110 through 113' Processing helix chain 'I' and resid 118 through 131 removed outlier: 3.627A pdb=" N ALA I 131 " --> pdb=" O MET I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 144 No H-bonds generated for 'chain 'I' and resid 142 through 144' Processing helix chain 'I' and resid 149 through 162 removed outlier: 4.059A pdb=" N ALA I 154 " --> pdb=" O LYS I 150 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU I 161 " --> pdb=" O ARG I 157 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASP I 162 " --> pdb=" O ALA I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 194 removed outlier: 3.574A pdb=" N LEU I 183 " --> pdb=" O ALA I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 211 removed outlier: 4.844A pdb=" N SER I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE I 211 " --> pdb=" O GLU I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 233 Processing helix chain 'I' and resid 238 through 244 Processing helix chain 'I' and resid 261 through 266 Processing helix chain 'J' and resid 47 through 54 Processing helix chain 'J' and resid 77 through 86 removed outlier: 3.873A pdb=" N ASP J 82 " --> pdb=" O GLY J 78 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS J 85 " --> pdb=" O PHE J 81 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN J 86 " --> pdb=" O ASP J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 107 Processing helix chain 'J' and resid 110 through 113 No H-bonds generated for 'chain 'J' and resid 110 through 113' Processing helix chain 'J' and resid 118 through 130 removed outlier: 3.856A pdb=" N ARG J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP J 123 " --> pdb=" O GLU J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 159 removed outlier: 4.088A pdb=" N ALA J 154 " --> pdb=" O LYS J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 194 removed outlier: 4.001A pdb=" N VAL J 182 " --> pdb=" O ILE J 178 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN J 191 " --> pdb=" O ILE J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 211 Processing helix chain 'J' and resid 229 through 233 Processing helix chain 'J' and resid 238 through 243 Processing helix chain 'J' and resid 263 through 266 No H-bonds generated for 'chain 'J' and resid 263 through 266' Processing helix chain 'K' and resid 23 through 33 removed outlier: 4.577A pdb=" N ALA K 27 " --> pdb=" O SER K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 56 through 72 removed outlier: 3.786A pdb=" N ILE K 66 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA K 69 " --> pdb=" O PHE K 65 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS K 71 " --> pdb=" O ARG K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 91 Processing helix chain 'L' and resid 24 through 33 removed outlier: 3.574A pdb=" N LEU L 28 " --> pdb=" O SER L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 38 No H-bonds generated for 'chain 'L' and resid 35 through 38' Processing helix chain 'L' and resid 56 through 72 removed outlier: 3.887A pdb=" N ILE L 66 " --> pdb=" O LEU L 62 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 92 removed outlier: 3.830A pdb=" N SER L 92 " --> pdb=" O ILE L 88 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 40 through 45 removed outlier: 3.769A pdb=" N THR A 79 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLU A 85 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL A 68 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.162A pdb=" N LEU A 60 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N THR A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 98 through 104 removed outlier: 3.817A pdb=" N ALA A 104 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLU A 109 " --> pdb=" O ALA A 104 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 39 through 46 removed outlier: 5.661A pdb=" N GLU B 85 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL B 68 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN B 87 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY B 66 " --> pdb=" O ASN B 87 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 99 through 103 Processing sheet with id= F, first strand: chain 'C' and resid 39 through 46 removed outlier: 6.459A pdb=" N GLU C 85 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL C 68 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN C 87 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY C 66 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL C 58 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 9.842A pdb=" N LYS C 57 " --> pdb=" O GLY C 108 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LYS C 110 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N THR C 59 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE C 112 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS C 110 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 102 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE C 112 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER C 100 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 114 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR C 98 " --> pdb=" O ILE C 114 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 41 through 46 removed outlier: 3.905A pdb=" N THR D 79 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP D 74 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLU D 85 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL D 68 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 98 through 103 Processing sheet with id= I, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.596A pdb=" N LEU D 60 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N THR D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 39 through 46 removed outlier: 6.482A pdb=" N GLU E 85 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL E 68 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 98 through 103 Processing sheet with id= L, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.034A pdb=" N LEU E 60 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N THR E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 40 through 46 removed outlier: 3.903A pdb=" N THR F 79 " --> pdb=" O ASP F 74 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU F 85 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 68 " --> pdb=" O GLU F 85 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 57 through 60 removed outlier: 3.927A pdb=" N GLY F 66 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU F 60 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N THR F 64 " --> pdb=" O LEU F 60 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 98 through 104 removed outlier: 3.720A pdb=" N ALA F 104 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU F 109 " --> pdb=" O ALA F 104 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 64 through 67 removed outlier: 4.045A pdb=" N GLU I 64 " --> pdb=" O LYS I 12 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS I 12 " --> pdb=" O GLU I 64 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE I 31 " --> pdb=" O ALA I 8 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU I 10 " --> pdb=" O VAL I 29 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL I 29 " --> pdb=" O GLU I 10 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 165 through 169 removed outlier: 6.385A pdb=" N THR I 197 " --> pdb=" O LEU I 166 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N TYR I 168 " --> pdb=" O THR I 197 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE I 199 " --> pdb=" O TYR I 168 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'J' and resid 9 through 12 removed outlier: 3.510A pdb=" N GLU J 64 " --> pdb=" O LYS J 12 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 226 through 228 removed outlier: 7.468A pdb=" N VAL J 36 " --> pdb=" O TYR J 214 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N TYR J 216 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY J 38 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N SER J 198 " --> pdb=" O THR J 37 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE J 39 " --> pdb=" O SER J 198 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL J 200 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY J 88 " --> pdb=" O ILE J 165 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'K' and resid 44 through 47 Processing sheet with id= U, first strand: chain 'L' and resid 45 through 47 removed outlier: 6.177A pdb=" N SER L 77 " --> pdb=" O VAL L 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= U 610 hydrogen bonds defined for protein. 1647 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: 4.10 Time building geometry restraints manager: 6.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2668 1.31 - 1.43: 3732 1.43 - 1.56: 9685 1.56 - 1.68: 4 1.68 - 1.81: 82 Bond restraints: 16171 Sorted by residual: bond pdb=" O4 LPP G 301 " pdb=" P1 LPP G 301 " ideal model delta sigma weight residual 1.510 1.606 -0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C29 LPP G 301 " pdb=" O27 LPP G 301 " ideal model delta sigma weight residual 1.399 1.329 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N PHE D 145 " pdb=" CA PHE D 145 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.00e-02 1.00e+04 8.76e+00 bond pdb=" N ILE G 81 " pdb=" CA ILE G 81 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.71e+00 bond pdb=" N VAL H 106 " pdb=" CA VAL H 106 " ideal model delta sigma weight residual 1.460 1.495 -0.034 1.19e-02 7.06e+03 8.38e+00 ... (remaining 16166 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.50: 221 105.50 - 112.64: 8987 112.64 - 119.78: 5071 119.78 - 126.92: 7502 126.92 - 134.05: 109 Bond angle restraints: 21890 Sorted by residual: angle pdb=" C ALA L 42 " pdb=" N GLU L 43 " pdb=" CA GLU L 43 " ideal model delta sigma weight residual 121.54 130.11 -8.57 1.91e+00 2.74e-01 2.01e+01 angle pdb=" N VAL I 138 " pdb=" CA VAL I 138 " pdb=" C VAL I 138 " ideal model delta sigma weight residual 112.98 108.33 4.65 1.25e+00 6.40e-01 1.38e+01 angle pdb=" N ILE F 142 " pdb=" CA ILE F 142 " pdb=" C ILE F 142 " ideal model delta sigma weight residual 113.42 109.09 4.33 1.17e+00 7.31e-01 1.37e+01 angle pdb=" N ASP H 254 " pdb=" CA ASP H 254 " pdb=" C ASP H 254 " ideal model delta sigma weight residual 111.14 107.28 3.86 1.08e+00 8.57e-01 1.28e+01 angle pdb=" N GLN H 93 " pdb=" CA GLN H 93 " pdb=" C GLN H 93 " ideal model delta sigma weight residual 113.21 109.17 4.04 1.15e+00 7.56e-01 1.23e+01 ... (remaining 21885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8239 17.99 - 35.98: 1021 35.98 - 53.98: 301 53.98 - 71.97: 71 71.97 - 89.96: 20 Dihedral angle restraints: 9652 sinusoidal: 3704 harmonic: 5948 Sorted by residual: dihedral pdb=" CA PHE H 213 " pdb=" C PHE H 213 " pdb=" N ALA H 214 " pdb=" CA ALA H 214 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA GLU L 43 " pdb=" C GLU L 43 " pdb=" N LEU L 44 " pdb=" CA LEU L 44 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LEU A 26 " pdb=" C LEU A 26 " pdb=" N ARG A 27 " pdb=" CA ARG A 27 " ideal model delta harmonic sigma weight residual 180.00 -158.11 -21.89 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 9649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1900 0.041 - 0.082: 569 0.082 - 0.123: 191 0.123 - 0.164: 20 0.164 - 0.205: 9 Chirality restraints: 2689 Sorted by residual: chirality pdb=" CA ILE C 142 " pdb=" N ILE C 142 " pdb=" C ILE C 142 " pdb=" CB ILE C 142 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE J 247 " pdb=" CA ILE J 247 " pdb=" CG1 ILE J 247 " pdb=" CG2 ILE J 247 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CA PHE G 213 " pdb=" N PHE G 213 " pdb=" C PHE G 213 " pdb=" CB PHE G 213 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.16e-01 ... (remaining 2686 not shown) Planarity restraints: 2753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 212 " -0.026 2.00e-02 2.50e+03 5.27e-02 2.77e+01 pdb=" C VAL G 212 " 0.091 2.00e-02 2.50e+03 pdb=" O VAL G 212 " -0.034 2.00e-02 2.50e+03 pdb=" N PHE G 213 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG G 101 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C ARG G 101 " 0.047 2.00e-02 2.50e+03 pdb=" O ARG G 101 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU G 102 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR J 256 " -0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO J 257 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO J 257 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 257 " -0.027 5.00e-02 4.00e+02 ... (remaining 2750 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 253 2.61 - 3.18: 15149 3.18 - 3.75: 25451 3.75 - 4.33: 33751 4.33 - 4.90: 54913 Nonbonded interactions: 129517 Sorted by model distance: nonbonded pdb=" OE1 GLN H 93 " pdb=" O28 LPP G 301 " model vdw 2.032 3.040 nonbonded pdb=" OG1 THR G 40 " pdb=" OG1 THR G 43 " model vdw 2.139 2.440 nonbonded pdb=" OG SER C 97 " pdb=" O SER C 115 " model vdw 2.145 2.440 nonbonded pdb=" OG1 THR G 121 " pdb=" O ALA G 221 " model vdw 2.157 2.440 nonbonded pdb=" N ASP E 76 " pdb=" OD1 ASP E 76 " model vdw 2.159 2.520 ... (remaining 129512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 or (resid 4 through 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 38 or (resid 39 and (name N or name CA \ or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 54 or (resid 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 or (resid 59 and \ (name N or name CA or name C or name O or name CB )) or resid 60 through 68 or \ (resid 69 through 70 and (name N or name CA or name C or name O or name CB )) or \ resid 71 through 72 or (resid 73 through 75 and (name N or name CA or name C or \ name O or name CB )) or resid 76 or (resid 77 through 78 and (name N or name CA \ or name C or name O or name CB )) or resid 79 through 91 or (resid 92 and (name \ N or name CA or name C or name O or name CB )) or resid 93 through 131 or (resi \ d 132 and (name N or name CA or name C or name O or name CB )) or resid 133 thro \ ugh 150)) selection = (chain 'B' and (resid 3 or (resid 4 through 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 54 or (resid 55 and (name N or name CA \ or name C or name O or name CB )) or resid 56 or (resid 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 or (resid 59 and (name N or nam \ e CA or name C or name O or name CB )) or resid 60 through 68 or (resid 69 throu \ gh 70 and (name N or name CA or name C or name O or name CB )) or resid 71 throu \ gh 77 or (resid 78 and (name N or name CA or name C or name O or name CB )) or r \ esid 79 through 91 or (resid 92 and (name N or name CA or name C or name O or na \ me CB )) or resid 93 through 150)) selection = (chain 'C' and (resid 3 or (resid 4 through 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 38 or (resid 39 and (name N or name CA \ or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 54 or (resid 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 or (resid 59 and \ (name N or name CA or name C or name O or name CB )) or resid 60 through 68 or \ (resid 69 through 70 and (name N or name CA or name C or name O or name CB )) or \ resid 71 through 72 or (resid 73 through 75 and (name N or name CA or name C or \ name O or name CB )) or resid 76 or (resid 77 through 78 and (name N or name CA \ or name C or name O or name CB )) or resid 79 through 131 or (resid 132 and (na \ me N or name CA or name C or name O or name CB )) or resid 133 through 150)) selection = (chain 'D' and (resid 3 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 38 or (resid 39 and (name N or name CA \ or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 54 or (resid 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 or (resid 59 and \ (name N or name CA or name C or name O or name CB )) or resid 60 through 68 or \ (resid 69 through 70 and (name N or name CA or name C or name O or name CB )) or \ resid 71 through 72 or (resid 73 through 75 and (name N or name CA or name C or \ name O or name CB )) or resid 76 or (resid 77 through 78 and (name N or name CA \ or name C or name O or name CB )) or resid 79 through 91 or (resid 92 and (name \ N or name CA or name C or name O or name CB )) or resid 93 through 131 or (resi \ d 132 and (name N or name CA or name C or name O or name CB )) or resid 133 thro \ ugh 150)) selection = (chain 'E' and (resid 3 or (resid 4 through 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 38 or (resid 39 and (name N or name CA \ or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 54 or (resid 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 or (resid 59 and \ (name N or name CA or name C or name O or name CB )) or resid 60 through 72 or \ (resid 73 through 75 and (name N or name CA or name C or name O or name CB )) or \ resid 76 or (resid 77 through 78 and (name N or name CA or name C or name O or \ name CB )) or resid 79 through 91 or (resid 92 and (name N or name CA or name C \ or name O or name CB )) or resid 93 through 131 or (resid 132 and (name N or nam \ e CA or name C or name O or name CB )) or resid 133 through 150)) selection = (chain 'F' and (resid 3 or (resid 4 through 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 38 or (resid 39 and (name N or name CA \ or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 68 or (resid 69 through \ 70 and (name N or name CA or name C or name O or name CB )) or resid 71 through \ 72 or (resid 73 through 75 and (name N or name CA or name C or name O or name C \ B )) or resid 76 or (resid 77 through 78 and (name N or name CA or name C or nam \ e O or name CB )) or resid 79 through 91 or (resid 92 and (name N or name CA or \ name C or name O or name CB )) or resid 93 through 131 or (resid 132 and (name N \ or name CA or name C or name O or name CB )) or resid 133 through 150)) } ncs_group { reference = (chain 'G' and (resid 5 through 100 or (resid 101 through 102 and (name N or nam \ e CA or name C or name O or name CB )) or resid 103 through 191 or (resid 192 an \ d (name N or name CA or name C or name O or name CB )) or resid 193 through 228 \ or (resid 229 and (name N or name CA or name C or name O or name CB )) or resid \ 231 through 262 or resid 301)) selection = (chain 'H' and (resid 5 through 185 or (resid 186 and (name N or name CA or name \ C or name O or name CB )) or resid 187 through 262 or (resid 301 and (name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22 or name C29 or name C30 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C6 or name C7 or name C8 \ or name O10 or name O2 or name O27 or name O28 or name O3 or name O4 or name O5 \ or name O9 or name P1 )))) } ncs_group { reference = (chain 'I' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 129 or (resid 130 through 131 and (n \ ame N or name CA or name C or name O or name CB )) or resid 132 through 134 or ( \ resid 135 and (name N or name CA or name C or name O or name CB )) or resid 136 \ through 215 or (resid 216 and (name N or name CA or name C or name O or name CB \ )) or resid 217 through 267)) selection = (chain 'J' and (resid 6 through 261 or (resid 262 through 263 and (name N or nam \ e CA or name C or name O or name CB )) or resid 264 through 267)) } ncs_group { reference = chain 'K' selection = chain 'L' } 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: 0.640 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: 4.570 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 42.470 Find NCS groups from input model: 1.060 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 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 : 0.005 0.096 16171 Z= 0.323 Angle : 0.825 10.472 21890 Z= 0.471 Chirality : 0.044 0.205 2689 Planarity : 0.004 0.053 2753 Dihedral : 18.106 89.959 5868 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 10.34 % Allowed : 27.08 % Favored : 62.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.14), residues: 2100 helix: -2.48 (0.14), residues: 857 sheet: -2.68 (0.27), residues: 294 loop : -3.65 (0.15), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 181 HIS 0.003 0.001 HIS I 203 PHE 0.019 0.002 PHE H 213 TYR 0.012 0.001 TYR D 111 ARG 0.003 0.000 ARG K 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 532 time to evaluate : 1.941 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: A 7 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8242 (mt-10) REVERT: A 86 ILE cc_start: 0.9285 (mp) cc_final: 0.9068 (mp) REVERT: A 110 LYS cc_start: 0.9281 (mtpp) cc_final: 0.9018 (mtpp) REVERT: A 124 LYS cc_start: 0.6503 (ttpp) cc_final: 0.6104 (mtpp) REVERT: B 7 GLU cc_start: 0.6653 (tt0) cc_final: 0.6304 (tm-30) REVERT: B 47 ASP cc_start: 0.8649 (t0) cc_final: 0.8427 (t0) REVERT: B 67 LYS cc_start: 0.8851 (ttmt) cc_final: 0.8364 (ttmt) REVERT: B 88 GLN cc_start: 0.8532 (mm110) cc_final: 0.8031 (mm110) REVERT: B 96 ASP cc_start: 0.7509 (p0) cc_final: 0.7083 (p0) REVERT: B 139 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7896 (tp30) REVERT: C 55 ARG cc_start: 0.7650 (ttt90) cc_final: 0.7000 (ttt90) REVERT: C 60 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8431 (tp) REVERT: C 111 TYR cc_start: 0.8730 (p90) cc_final: 0.8385 (p90) REVERT: C 139 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8280 (tp30) REVERT: C 145 PHE cc_start: 0.7742 (m-80) cc_final: 0.7520 (m-10) REVERT: D 27 ARG cc_start: 0.8371 (mtt180) cc_final: 0.7146 (mtp180) REVERT: D 144 LYS cc_start: 0.9067 (ptmm) cc_final: 0.8758 (ptmm) REVERT: D 145 PHE cc_start: 0.8323 (m-80) cc_final: 0.7872 (m-80) REVERT: E 49 ILE cc_start: 0.8759 (pt) cc_final: 0.8538 (pt) REVERT: E 145 PHE cc_start: 0.8077 (m-80) cc_final: 0.7608 (m-80) REVERT: F 67 LYS cc_start: 0.8762 (ptpt) cc_final: 0.8341 (ptmt) REVERT: F 110 LYS cc_start: 0.9041 (mttm) cc_final: 0.8771 (mtpt) REVERT: F 145 PHE cc_start: 0.7439 (m-80) cc_final: 0.7212 (m-80) REVERT: G 80 ASN cc_start: 0.9051 (t0) cc_final: 0.8724 (t0) REVERT: G 94 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7831 (ttt) REVERT: G 132 GLN cc_start: 0.8748 (tt0) cc_final: 0.8459 (tt0) REVERT: G 159 MET cc_start: 0.8547 (tpt) cc_final: 0.7874 (tpt) REVERT: G 161 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8772 (mm) REVERT: G 165 ILE cc_start: 0.8686 (mt) cc_final: 0.8336 (mp) REVERT: G 176 MET cc_start: 0.8552 (tmm) cc_final: 0.8106 (tmm) REVERT: G 201 GLU cc_start: 0.8150 (tp30) cc_final: 0.7730 (tp30) REVERT: G 227 ASP cc_start: 0.8094 (t70) cc_final: 0.7442 (t0) REVERT: G 233 GLU cc_start: 0.8279 (tp30) cc_final: 0.7959 (tp30) REVERT: H 8 GLU cc_start: 0.7806 (tt0) cc_final: 0.7355 (pt0) REVERT: H 9 ARG cc_start: 0.6639 (tpp80) cc_final: 0.5905 (ptt90) REVERT: H 85 TYR cc_start: 0.7557 (m-80) cc_final: 0.7335 (m-80) REVERT: H 94 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8468 (ttt) REVERT: H 126 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8277 (t0) REVERT: H 227 ASP cc_start: 0.8253 (t0) cc_final: 0.7636 (t0) REVERT: I 12 LYS cc_start: 0.7925 (mptp) cc_final: 0.7574 (mttt) REVERT: I 35 LYS cc_start: 0.8413 (mmpt) cc_final: 0.8043 (mptt) REVERT: I 75 LEU cc_start: 0.8451 (mt) cc_final: 0.8223 (mt) REVERT: I 202 SER cc_start: 0.8427 (OUTLIER) cc_final: 0.7749 (p) REVERT: J 62 LYS cc_start: 0.8913 (pttp) cc_final: 0.8608 (tppt) REVERT: J 64 GLU cc_start: 0.6633 (pm20) cc_final: 0.6350 (pm20) REVERT: J 165 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8554 (pt) REVERT: J 172 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8579 (p90) REVERT: J 242 GLN cc_start: 0.7909 (tt0) cc_final: 0.7539 (tt0) REVERT: K 8 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7072 (tp30) REVERT: K 52 GLU cc_start: 0.8396 (pt0) cc_final: 0.7719 (tt0) REVERT: K 65 PHE cc_start: 0.8991 (m-10) cc_final: 0.8567 (m-10) REVERT: K 90 LYS cc_start: 0.8553 (ttpp) cc_final: 0.7867 (mmpt) REVERT: L 15 GLN cc_start: 0.6666 (pt0) cc_final: 0.6248 (pp30) REVERT: L 29 ARG cc_start: 0.8957 (tmt-80) cc_final: 0.8741 (tpt90) REVERT: L 31 GLN cc_start: 0.8342 (pt0) cc_final: 0.8082 (pt0) REVERT: L 37 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7462 (tmm160) REVERT: L 53 ARG cc_start: 0.8051 (ttp80) cc_final: 0.7706 (ptm-80) REVERT: L 70 ARG cc_start: 0.7949 (ttt-90) cc_final: 0.7673 (ttp-110) outliers start: 173 outliers final: 121 residues processed: 670 average time/residue: 0.3029 time to fit residues: 289.3081 Evaluate side-chains 555 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 426 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 118 SER Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 203 HIS Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 84 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 53 optimal weight: 0.3980 chunk 104 optimal weight: 0.3980 chunk 83 optimal weight: 6.9990 chunk 160 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 186 optimal weight: 0.0010 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN C 35 ASN C 148 ASN E 92 ASN E 133 GLN F 88 GLN G 89 GLN G 93 GLN G 224 GLN ** H 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 GLN ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN I 191 ASN J 191 ASN J 255 HIS L 31 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16171 Z= 0.175 Angle : 0.650 8.928 21890 Z= 0.327 Chirality : 0.043 0.194 2689 Planarity : 0.004 0.046 2753 Dihedral : 11.849 65.542 2629 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 9.15 % Allowed : 29.47 % Favored : 61.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.16), residues: 2100 helix: -1.21 (0.17), residues: 842 sheet: -2.42 (0.27), residues: 290 loop : -3.13 (0.16), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 66 HIS 0.002 0.001 HIS I 255 PHE 0.015 0.002 PHE H 213 TYR 0.019 0.001 TYR F 111 ARG 0.005 0.000 ARG I 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 483 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8172 (p0) cc_final: 0.7950 (p0) REVERT: A 124 LYS cc_start: 0.6573 (ttpp) cc_final: 0.6154 (mtpp) REVERT: B 7 GLU cc_start: 0.6618 (tt0) cc_final: 0.6303 (tm-30) REVERT: B 47 ASP cc_start: 0.8596 (t0) cc_final: 0.8304 (t0) REVERT: B 67 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8485 (ttmt) REVERT: B 88 GLN cc_start: 0.8530 (mm110) cc_final: 0.8267 (mm110) REVERT: B 139 GLU cc_start: 0.8539 (mm-30) cc_final: 0.7897 (tp30) REVERT: C 7 GLU cc_start: 0.6728 (tp30) cc_final: 0.6017 (pt0) REVERT: C 43 TYR cc_start: 0.8446 (m-10) cc_final: 0.8137 (m-80) REVERT: C 74 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7334 (p0) REVERT: C 144 LYS cc_start: 0.8708 (ptmm) cc_final: 0.8450 (ptmt) REVERT: C 145 PHE cc_start: 0.7470 (m-80) cc_final: 0.7247 (m-10) REVERT: D 27 ARG cc_start: 0.8439 (mtt180) cc_final: 0.7181 (mtp180) REVERT: D 45 TYR cc_start: 0.8366 (m-10) cc_final: 0.8072 (m-10) REVERT: D 144 LYS cc_start: 0.8962 (ptmm) cc_final: 0.8669 (ptmm) REVERT: D 145 PHE cc_start: 0.8256 (m-80) cc_final: 0.7818 (m-80) REVERT: F 47 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7760 (t0) REVERT: F 125 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7210 (t70) REVERT: G 80 ASN cc_start: 0.8910 (t0) cc_final: 0.8612 (t0) REVERT: G 94 MET cc_start: 0.8388 (tmm) cc_final: 0.7991 (ttt) REVERT: G 165 ILE cc_start: 0.8628 (mt) cc_final: 0.8254 (mp) REVERT: G 176 MET cc_start: 0.8438 (tmm) cc_final: 0.7988 (tmm) REVERT: G 227 ASP cc_start: 0.7896 (t70) cc_final: 0.7293 (t0) REVERT: H 8 GLU cc_start: 0.7854 (tt0) cc_final: 0.7428 (pt0) REVERT: H 9 ARG cc_start: 0.6459 (tpp80) cc_final: 0.5768 (ptt90) REVERT: H 94 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8415 (ttt) REVERT: H 227 ASP cc_start: 0.8217 (t0) cc_final: 0.7470 (t0) REVERT: I 12 LYS cc_start: 0.7907 (mptp) cc_final: 0.7613 (mttt) REVERT: I 35 LYS cc_start: 0.8324 (mmpt) cc_final: 0.7969 (mptt) REVERT: I 57 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: I 58 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8309 (mt) REVERT: I 75 LEU cc_start: 0.8262 (mt) cc_final: 0.8036 (mt) REVERT: I 101 ASP cc_start: 0.8238 (p0) cc_final: 0.8009 (p0) REVERT: I 105 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.7843 (m-40) REVERT: J 57 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: J 62 LYS cc_start: 0.8804 (pttp) cc_final: 0.8562 (tppt) REVERT: J 144 GLU cc_start: 0.7622 (mp0) cc_final: 0.7414 (pt0) REVERT: K 8 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7114 (tm-30) REVERT: K 34 ARG cc_start: 0.6950 (mtp85) cc_final: 0.6701 (mtp85) REVERT: K 52 GLU cc_start: 0.8448 (pt0) cc_final: 0.7744 (tt0) REVERT: K 87 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: K 90 LYS cc_start: 0.8561 (ttpp) cc_final: 0.7806 (mmpt) REVERT: L 15 GLN cc_start: 0.6617 (pt0) cc_final: 0.6359 (pp30) REVERT: L 53 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7734 (ptm-80) REVERT: L 70 ARG cc_start: 0.7887 (ttt-90) cc_final: 0.7667 (ttp-170) outliers start: 153 outliers final: 88 residues processed: 591 average time/residue: 0.2882 time to fit residues: 246.5263 Evaluate side-chains 517 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 419 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 57 GLN Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 203 HIS Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 81 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 63 optimal weight: 0.0970 chunk 149 optimal weight: 3.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN D 133 GLN E 133 GLN ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16171 Z= 0.283 Angle : 0.679 10.568 21890 Z= 0.343 Chirality : 0.044 0.200 2689 Planarity : 0.004 0.047 2753 Dihedral : 10.510 59.898 2529 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 10.28 % Allowed : 31.44 % Favored : 58.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.17), residues: 2100 helix: -0.84 (0.17), residues: 848 sheet: -2.01 (0.29), residues: 274 loop : -3.06 (0.16), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 219 HIS 0.005 0.001 HIS I 113 PHE 0.023 0.002 PHE C 13 TYR 0.017 0.001 TYR A 111 ARG 0.005 0.000 ARG I 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 440 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.6619 (ttpp) cc_final: 0.6188 (mtpp) REVERT: B 7 GLU cc_start: 0.6661 (tt0) cc_final: 0.6330 (tm-30) REVERT: B 47 ASP cc_start: 0.8608 (t0) cc_final: 0.8344 (t0) REVERT: B 67 LYS cc_start: 0.8823 (ttmt) cc_final: 0.8434 (ttmt) REVERT: B 85 GLU cc_start: 0.7928 (tp30) cc_final: 0.7701 (tp30) REVERT: B 88 GLN cc_start: 0.8409 (mm110) cc_final: 0.8108 (mm110) REVERT: B 139 GLU cc_start: 0.8685 (mm-30) cc_final: 0.7950 (tp30) REVERT: B 144 LYS cc_start: 0.8552 (ptmt) cc_final: 0.8306 (ptmm) REVERT: C 7 GLU cc_start: 0.6857 (tp30) cc_final: 0.6074 (pt0) REVERT: C 59 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8869 (t) REVERT: C 67 LYS cc_start: 0.8670 (tptt) cc_final: 0.8319 (tptt) REVERT: C 145 PHE cc_start: 0.7580 (m-80) cc_final: 0.7277 (m-80) REVERT: D 27 ARG cc_start: 0.8315 (mtt180) cc_final: 0.7071 (mtp180) REVERT: D 144 LYS cc_start: 0.8954 (ptmm) cc_final: 0.8639 (ptmm) REVERT: D 145 PHE cc_start: 0.8351 (m-80) cc_final: 0.7855 (m-80) REVERT: E 13 PHE cc_start: 0.6972 (m-80) cc_final: 0.6703 (m-10) REVERT: G 36 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8759 (pp) REVERT: G 50 LYS cc_start: 0.9055 (tptp) cc_final: 0.8842 (tptm) REVERT: G 80 ASN cc_start: 0.8933 (t0) cc_final: 0.8565 (t0) REVERT: G 132 GLN cc_start: 0.8753 (tt0) cc_final: 0.8475 (tt0) REVERT: G 165 ILE cc_start: 0.8638 (mt) cc_final: 0.8260 (mp) REVERT: G 176 MET cc_start: 0.8570 (tmm) cc_final: 0.8079 (tmm) REVERT: G 204 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8703 (tt) REVERT: G 227 ASP cc_start: 0.7907 (t70) cc_final: 0.7286 (t0) REVERT: H 8 GLU cc_start: 0.7853 (tt0) cc_final: 0.7435 (pt0) REVERT: H 9 ARG cc_start: 0.6409 (tpp80) cc_final: 0.5588 (ptm-80) REVERT: H 93 GLN cc_start: 0.8461 (tt0) cc_final: 0.8175 (tt0) REVERT: H 227 ASP cc_start: 0.8030 (t0) cc_final: 0.7436 (t0) REVERT: I 12 LYS cc_start: 0.7893 (mptp) cc_final: 0.7611 (mttt) REVERT: I 35 LYS cc_start: 0.8358 (mmpt) cc_final: 0.8028 (mptt) REVERT: I 57 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: I 58 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8077 (mt) REVERT: I 71 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8227 (p0) REVERT: I 75 LEU cc_start: 0.8279 (mt) cc_final: 0.8005 (mt) REVERT: J 57 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8435 (tp40) REVERT: J 62 LYS cc_start: 0.8802 (pttp) cc_final: 0.8563 (tppt) REVERT: J 262 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8697 (tpt-90) REVERT: K 13 GLU cc_start: 0.6808 (pm20) cc_final: 0.6497 (pm20) REVERT: K 34 ARG cc_start: 0.7064 (mtp85) cc_final: 0.6854 (mtp85) REVERT: K 52 GLU cc_start: 0.8482 (pt0) cc_final: 0.7767 (tt0) REVERT: K 90 LYS cc_start: 0.8633 (ttpp) cc_final: 0.7886 (mmpt) REVERT: L 15 GLN cc_start: 0.6990 (pt0) cc_final: 0.6616 (pp30) REVERT: L 31 GLN cc_start: 0.8136 (pt0) cc_final: 0.7621 (pp30) REVERT: L 53 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7686 (ptm-80) outliers start: 172 outliers final: 125 residues processed: 558 average time/residue: 0.2947 time to fit residues: 236.7681 Evaluate side-chains 536 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 403 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 258 THR Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 68 ASN Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 57 GLN Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 203 HIS Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain J residue 262 ARG Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 96 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 89 optimal weight: 0.5980 chunk 125 optimal weight: 4.9990 chunk 187 optimal weight: 0.0000 chunk 198 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 177 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN E 133 GLN ** H 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16171 Z= 0.173 Angle : 0.641 9.907 21890 Z= 0.320 Chirality : 0.043 0.200 2689 Planarity : 0.004 0.047 2753 Dihedral : 9.788 59.915 2518 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 8.73 % Allowed : 33.89 % Favored : 57.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.17), residues: 2100 helix: -0.52 (0.18), residues: 853 sheet: -1.88 (0.30), residues: 262 loop : -2.87 (0.17), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 66 HIS 0.002 0.000 HIS I 255 PHE 0.044 0.002 PHE C 13 TYR 0.018 0.001 TYR A 111 ARG 0.006 0.000 ARG I 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 455 time to evaluate : 1.942 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: A 72 ASP cc_start: 0.8171 (p0) cc_final: 0.7930 (p0) REVERT: A 124 LYS cc_start: 0.6615 (ttpp) cc_final: 0.6323 (mtpp) REVERT: B 7 GLU cc_start: 0.6574 (tt0) cc_final: 0.6317 (tm-30) REVERT: B 47 ASP cc_start: 0.8533 (t0) cc_final: 0.8188 (t0) REVERT: B 67 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8431 (ttmt) REVERT: B 85 GLU cc_start: 0.7932 (tp30) cc_final: 0.7647 (tp30) REVERT: B 86 ILE cc_start: 0.8913 (mp) cc_final: 0.8592 (mp) REVERT: B 139 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8076 (tp30) REVERT: C 55 ARG cc_start: 0.7606 (ttt90) cc_final: 0.7054 (ttt180) REVERT: C 67 LYS cc_start: 0.8473 (tptt) cc_final: 0.8085 (tptt) REVERT: C 140 ASP cc_start: 0.8649 (m-30) cc_final: 0.8082 (t0) REVERT: C 144 LYS cc_start: 0.8551 (ptmm) cc_final: 0.8271 (ptmt) REVERT: C 145 PHE cc_start: 0.7409 (m-80) cc_final: 0.7124 (m-80) REVERT: D 27 ARG cc_start: 0.8273 (mtt180) cc_final: 0.7084 (mtp180) REVERT: D 57 LYS cc_start: 0.8641 (mmtm) cc_final: 0.7958 (mtmm) REVERT: D 125 ASP cc_start: 0.6348 (OUTLIER) cc_final: 0.6084 (t70) REVERT: D 144 LYS cc_start: 0.8904 (ptmm) cc_final: 0.8427 (ptmm) REVERT: D 145 PHE cc_start: 0.8282 (m-80) cc_final: 0.7635 (m-80) REVERT: E 13 PHE cc_start: 0.6998 (m-10) cc_final: 0.6704 (m-10) REVERT: E 88 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7718 (tp-100) REVERT: G 80 ASN cc_start: 0.8819 (t0) cc_final: 0.8501 (t0) REVERT: G 131 GLU cc_start: 0.7859 (mp0) cc_final: 0.7210 (mp0) REVERT: G 132 GLN cc_start: 0.8424 (tt0) cc_final: 0.8111 (tt0) REVERT: G 165 ILE cc_start: 0.8578 (mt) cc_final: 0.8195 (mp) REVERT: G 176 MET cc_start: 0.8420 (tmm) cc_final: 0.8178 (tmm) REVERT: G 193 MET cc_start: 0.7689 (ttp) cc_final: 0.7457 (ttp) REVERT: G 201 GLU cc_start: 0.8502 (tp30) cc_final: 0.8216 (tp30) REVERT: G 227 ASP cc_start: 0.7758 (t70) cc_final: 0.7170 (t0) REVERT: H 8 GLU cc_start: 0.7857 (tt0) cc_final: 0.7417 (pt0) REVERT: H 9 ARG cc_start: 0.6390 (tpp80) cc_final: 0.5544 (ptm-80) REVERT: H 58 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8820 (mp) REVERT: H 93 GLN cc_start: 0.8378 (tt0) cc_final: 0.8116 (tt0) REVERT: H 227 ASP cc_start: 0.8093 (t0) cc_final: 0.7387 (t0) REVERT: H 262 PHE cc_start: 0.7037 (OUTLIER) cc_final: 0.5667 (m-80) REVERT: I 12 LYS cc_start: 0.7896 (mptp) cc_final: 0.7652 (mttt) REVERT: I 35 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8058 (mptt) REVERT: I 57 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: I 58 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.7700 (mt) REVERT: I 71 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8356 (p0) REVERT: I 75 LEU cc_start: 0.8233 (mt) cc_final: 0.7987 (mt) REVERT: I 100 LEU cc_start: 0.9275 (mt) cc_final: 0.9055 (mp) REVERT: I 101 ASP cc_start: 0.8175 (p0) cc_final: 0.7847 (p0) REVERT: I 105 ASN cc_start: 0.8293 (t160) cc_final: 0.7632 (m-40) REVERT: J 57 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8427 (tp40) REVERT: J 62 LYS cc_start: 0.8792 (pttp) cc_final: 0.8561 (tppt) REVERT: J 144 GLU cc_start: 0.7689 (mp0) cc_final: 0.7397 (mt-10) REVERT: J 243 PHE cc_start: 0.8619 (t80) cc_final: 0.8350 (t80) REVERT: K 52 GLU cc_start: 0.8465 (pt0) cc_final: 0.7740 (tt0) REVERT: K 90 LYS cc_start: 0.8642 (ttpp) cc_final: 0.7829 (mmpt) REVERT: L 15 GLN cc_start: 0.6854 (pt0) cc_final: 0.6621 (pp30) REVERT: L 37 ARG cc_start: 0.8182 (tmm160) cc_final: 0.7675 (tmm-80) REVERT: L 53 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7659 (ptm-80) outliers start: 146 outliers final: 103 residues processed: 557 average time/residue: 0.3197 time to fit residues: 260.0150 Evaluate side-chains 532 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 420 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 262 PHE Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 57 GLN Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.1084 > 50: distance: 58 - 64: 31.653 distance: 64 - 65: 5.766 distance: 64 - 129: 52.248 distance: 65 - 66: 48.278 distance: 65 - 68: 39.705 distance: 66 - 67: 12.057 distance: 66 - 72: 33.891 distance: 67 - 126: 45.252 distance: 68 - 69: 24.024 distance: 69 - 70: 22.163 distance: 69 - 71: 22.109 distance: 72 - 73: 5.519 distance: 73 - 74: 14.271 distance: 73 - 76: 4.951 distance: 74 - 75: 30.011 distance: 74 - 79: 29.875 distance: 76 - 77: 47.325 distance: 76 - 78: 38.978 distance: 79 - 80: 26.623 distance: 80 - 81: 21.694 distance: 80 - 83: 20.503 distance: 81 - 82: 19.003 distance: 81 - 84: 18.739 distance: 84 - 85: 11.959 distance: 85 - 86: 8.040 distance: 86 - 88: 18.077 distance: 88 - 89: 20.588 distance: 89 - 90: 20.907 distance: 89 - 92: 17.003 distance: 90 - 91: 40.903 distance: 90 - 96: 18.577 distance: 92 - 93: 13.325 distance: 93 - 94: 23.806 distance: 93 - 95: 18.861 distance: 96 - 97: 31.770 distance: 97 - 98: 12.960 distance: 97 - 100: 24.181 distance: 98 - 99: 13.428 distance: 98 - 104: 35.174 distance: 100 - 101: 24.266 distance: 101 - 102: 14.157 distance: 101 - 103: 14.403 distance: 104 - 105: 24.041 distance: 105 - 106: 30.819 distance: 106 - 107: 42.151 distance: 106 - 108: 50.235 distance: 108 - 109: 21.838 distance: 109 - 110: 17.515 distance: 109 - 112: 32.086 distance: 110 - 111: 29.267 distance: 110 - 117: 41.703 distance: 112 - 113: 29.284 distance: 113 - 114: 19.592 distance: 114 - 115: 9.474 distance: 117 - 118: 35.994 distance: 118 - 119: 11.879 distance: 118 - 121: 12.984 distance: 119 - 120: 21.196 distance: 119 - 126: 24.358 distance: 121 - 122: 19.634 distance: 122 - 123: 9.025 distance: 123 - 124: 20.005 distance: 124 - 125: 8.257 distance: 126 - 127: 17.609 distance: 127 - 128: 12.291 distance: 127 - 130: 37.468 distance: 128 - 129: 26.909 distance: 128 - 138: 14.768 distance: 130 - 131: 8.723 distance: 131 - 132: 32.988 distance: 131 - 133: 8.502 distance: 132 - 134: 22.298 distance: 133 - 135: 13.368 distance: 134 - 136: 11.449 distance: 135 - 136: 28.950 distance: 136 - 137: 18.087