Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 13 01:57:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmr_40231/08_2023/8gmr_40231_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmr_40231/08_2023/8gmr_40231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmr_40231/08_2023/8gmr_40231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmr_40231/08_2023/8gmr_40231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmr_40231/08_2023/8gmr_40231_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmr_40231/08_2023/8gmr_40231_trim_updated.pdb" } resolution = 3.76 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= -0.010 sd= 0.445 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 8 5.49 5 S 96 5.16 5 C 8176 2.51 5 N 2048 2.21 5 O 2144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 12472 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1507 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "A" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1507 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "C" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1507 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "D" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1507 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "E" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1507 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "F" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1507 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "G" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1507 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "H" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1507 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.04, per 1000 atoms: 0.56 Number of scatterers: 12472 At special positions: 0 Unit cell: (127.544, 127.544, 97.584, 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 96 16.00 P 8 15.00 O 2144 8.00 N 2048 7.00 C 8176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 127 " distance=2.03 Simple disulfide: pdb=" SG CYS F 42 " - pdb=" SG CYS F 127 " distance=2.03 Simple disulfide: pdb=" SG CYS G 42 " - pdb=" SG CYS G 127 " distance=2.03 Simple disulfide: pdb=" SG CYS H 42 " - pdb=" SG CYS H 127 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.29 Conformation dependent library (CDL) restraints added in 1.9 seconds 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3296 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 0 sheets defined 60.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'B' and resid 34 through 37 No H-bonds generated for 'chain 'B' and resid 34 through 37' Processing helix chain 'B' and resid 49 through 70 removed outlier: 3.556A pdb=" N ILE B 56 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Proline residue: B 60 - end of helix removed outlier: 4.119A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 83 removed outlier: 3.893A pdb=" N GLU B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 110 through 121 removed outlier: 4.428A pdb=" N THR B 118 " --> pdb=" O TRP B 114 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 126 No H-bonds generated for 'chain 'B' and resid 123 through 126' Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 149 through 158 removed outlier: 4.812A pdb=" N ARG B 158 " --> pdb=" O ARG B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 214 through 220 removed outlier: 3.925A pdb=" N TRP B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 250 removed outlier: 4.002A pdb=" N GLU B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 241 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE B 242 " --> pdb=" O HIS B 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE B 250 " --> pdb=" O CYS B 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 37 No H-bonds generated for 'chain 'A' and resid 34 through 37' Processing helix chain 'A' and resid 49 through 70 removed outlier: 3.556A pdb=" N ILE A 56 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 4.119A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 83 removed outlier: 3.893A pdb=" N GLU A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 110 through 121 removed outlier: 4.428A pdb=" N THR A 118 " --> pdb=" O TRP A 114 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 126 No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 129 through 132 Processing helix chain 'A' and resid 149 through 158 removed outlier: 4.812A pdb=" N ARG A 158 " --> pdb=" O ARG A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 176 No H-bonds generated for 'chain 'A' and resid 173 through 176' Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 214 through 220 removed outlier: 3.925A pdb=" N TRP A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 250 removed outlier: 4.002A pdb=" N GLU A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE A 242 " --> pdb=" O HIS A 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE A 250 " --> pdb=" O CYS A 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 37 No H-bonds generated for 'chain 'C' and resid 34 through 37' Processing helix chain 'C' and resid 49 through 70 removed outlier: 3.556A pdb=" N ILE C 56 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 57 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Proline residue: C 60 - end of helix removed outlier: 4.119A pdb=" N VAL C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 83 removed outlier: 3.893A pdb=" N GLU C 80 " --> pdb=" O SER C 76 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 110 through 121 removed outlier: 4.428A pdb=" N THR C 118 " --> pdb=" O TRP C 114 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 No H-bonds generated for 'chain 'C' and resid 123 through 126' Processing helix chain 'C' and resid 129 through 132 Processing helix chain 'C' and resid 149 through 158 removed outlier: 4.812A pdb=" N ARG C 158 " --> pdb=" O ARG C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 180 through 196 Processing helix chain 'C' and resid 198 through 200 No H-bonds generated for 'chain 'C' and resid 198 through 200' Processing helix chain 'C' and resid 214 through 220 removed outlier: 3.925A pdb=" N TRP C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 250 removed outlier: 4.002A pdb=" N GLU C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 240 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 241 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE C 242 " --> pdb=" O HIS C 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN C 249 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE C 250 " --> pdb=" O CYS C 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 37 No H-bonds generated for 'chain 'D' and resid 34 through 37' Processing helix chain 'D' and resid 49 through 70 removed outlier: 3.556A pdb=" N ILE D 56 " --> pdb=" O TYR D 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 57 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Proline residue: D 60 - end of helix removed outlier: 4.119A pdb=" N VAL D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 83 removed outlier: 3.893A pdb=" N GLU D 80 " --> pdb=" O SER D 76 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 110 through 121 removed outlier: 4.428A pdb=" N THR D 118 " --> pdb=" O TRP D 114 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 126 No H-bonds generated for 'chain 'D' and resid 123 through 126' Processing helix chain 'D' and resid 129 through 132 Processing helix chain 'D' and resid 149 through 158 removed outlier: 4.812A pdb=" N ARG D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 176 No H-bonds generated for 'chain 'D' and resid 173 through 176' Processing helix chain 'D' and resid 180 through 196 Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 214 through 220 removed outlier: 3.925A pdb=" N TRP D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 250 removed outlier: 4.002A pdb=" N GLU D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 240 " --> pdb=" O THR D 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 241 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE D 242 " --> pdb=" O HIS D 238 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN D 249 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE D 250 " --> pdb=" O CYS D 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 37 No H-bonds generated for 'chain 'E' and resid 34 through 37' Processing helix chain 'E' and resid 49 through 70 removed outlier: 3.556A pdb=" N ILE E 56 " --> pdb=" O TYR E 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU E 57 " --> pdb=" O SER E 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Proline residue: E 60 - end of helix removed outlier: 4.119A pdb=" N VAL E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 83 removed outlier: 3.893A pdb=" N GLU E 80 " --> pdb=" O SER E 76 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP E 82 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 110 through 121 removed outlier: 4.428A pdb=" N THR E 118 " --> pdb=" O TRP E 114 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU E 119 " --> pdb=" O VAL E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 126 No H-bonds generated for 'chain 'E' and resid 123 through 126' Processing helix chain 'E' and resid 129 through 132 Processing helix chain 'E' and resid 149 through 158 removed outlier: 4.812A pdb=" N ARG E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 176 No H-bonds generated for 'chain 'E' and resid 173 through 176' Processing helix chain 'E' and resid 180 through 196 Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 214 through 220 removed outlier: 3.925A pdb=" N TRP E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 250 removed outlier: 4.002A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS E 240 " --> pdb=" O THR E 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 241 " --> pdb=" O GLU E 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE E 242 " --> pdb=" O HIS E 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS E 244 " --> pdb=" O LYS E 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN E 248 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN E 249 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE E 250 " --> pdb=" O CYS E 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 37 No H-bonds generated for 'chain 'F' and resid 34 through 37' Processing helix chain 'F' and resid 49 through 70 removed outlier: 3.556A pdb=" N ILE F 56 " --> pdb=" O TYR F 52 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU F 57 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Proline residue: F 60 - end of helix removed outlier: 4.119A pdb=" N VAL F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 83 removed outlier: 3.893A pdb=" N GLU F 80 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP F 82 " --> pdb=" O LEU F 78 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 106 Processing helix chain 'F' and resid 110 through 121 removed outlier: 4.428A pdb=" N THR F 118 " --> pdb=" O TRP F 114 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU F 119 " --> pdb=" O VAL F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 126 No H-bonds generated for 'chain 'F' and resid 123 through 126' Processing helix chain 'F' and resid 129 through 132 Processing helix chain 'F' and resid 149 through 158 removed outlier: 4.812A pdb=" N ARG F 158 " --> pdb=" O ARG F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 176 No H-bonds generated for 'chain 'F' and resid 173 through 176' Processing helix chain 'F' and resid 180 through 196 Processing helix chain 'F' and resid 198 through 200 No H-bonds generated for 'chain 'F' and resid 198 through 200' Processing helix chain 'F' and resid 214 through 220 removed outlier: 3.925A pdb=" N TRP F 220 " --> pdb=" O LYS F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 250 removed outlier: 4.002A pdb=" N GLU F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR F 234 " --> pdb=" O LEU F 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS F 240 " --> pdb=" O THR F 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 241 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE F 242 " --> pdb=" O HIS F 238 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS F 244 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLN F 249 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE F 250 " --> pdb=" O CYS F 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 37 No H-bonds generated for 'chain 'G' and resid 34 through 37' Processing helix chain 'G' and resid 49 through 70 removed outlier: 3.556A pdb=" N ILE G 56 " --> pdb=" O TYR G 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU G 57 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Proline residue: G 60 - end of helix removed outlier: 4.119A pdb=" N VAL G 70 " --> pdb=" O LEU G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 83 removed outlier: 3.893A pdb=" N GLU G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 106 Processing helix chain 'G' and resid 110 through 121 removed outlier: 4.428A pdb=" N THR G 118 " --> pdb=" O TRP G 114 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU G 119 " --> pdb=" O VAL G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 126 No H-bonds generated for 'chain 'G' and resid 123 through 126' Processing helix chain 'G' and resid 129 through 132 Processing helix chain 'G' and resid 149 through 158 removed outlier: 4.812A pdb=" N ARG G 158 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 176 No H-bonds generated for 'chain 'G' and resid 173 through 176' Processing helix chain 'G' and resid 180 through 196 Processing helix chain 'G' and resid 198 through 200 No H-bonds generated for 'chain 'G' and resid 198 through 200' Processing helix chain 'G' and resid 214 through 220 removed outlier: 3.925A pdb=" N TRP G 220 " --> pdb=" O LYS G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 250 removed outlier: 4.003A pdb=" N GLU G 233 " --> pdb=" O LYS G 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR G 234 " --> pdb=" O LEU G 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS G 240 " --> pdb=" O THR G 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA G 241 " --> pdb=" O GLU G 237 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE G 242 " --> pdb=" O HIS G 238 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS G 244 " --> pdb=" O LYS G 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL G 245 " --> pdb=" O ALA G 241 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN G 249 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE G 250 " --> pdb=" O CYS G 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 37 No H-bonds generated for 'chain 'H' and resid 34 through 37' Processing helix chain 'H' and resid 49 through 70 removed outlier: 3.556A pdb=" N ILE H 56 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) Proline residue: H 60 - end of helix removed outlier: 4.119A pdb=" N VAL H 70 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 83 removed outlier: 3.893A pdb=" N GLU H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 106 Processing helix chain 'H' and resid 110 through 121 removed outlier: 4.428A pdb=" N THR H 118 " --> pdb=" O TRP H 114 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU H 119 " --> pdb=" O VAL H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 126 No H-bonds generated for 'chain 'H' and resid 123 through 126' Processing helix chain 'H' and resid 129 through 132 Processing helix chain 'H' and resid 149 through 158 removed outlier: 4.811A pdb=" N ARG H 158 " --> pdb=" O ARG H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 176 No H-bonds generated for 'chain 'H' and resid 173 through 176' Processing helix chain 'H' and resid 180 through 196 Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'H' and resid 214 through 220 removed outlier: 3.925A pdb=" N TRP H 220 " --> pdb=" O LYS H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 250 removed outlier: 4.002A pdb=" N GLU H 233 " --> pdb=" O LYS H 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR H 234 " --> pdb=" O LEU H 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS H 240 " --> pdb=" O THR H 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA H 241 " --> pdb=" O GLU H 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE H 242 " --> pdb=" O HIS H 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS H 244 " --> pdb=" O LYS H 240 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL H 245 " --> pdb=" O ALA H 241 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN H 248 " --> pdb=" O LYS H 244 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLN H 249 " --> pdb=" O VAL H 245 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE H 250 " --> pdb=" O CYS H 246 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 5.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1904 1.31 - 1.44: 3312 1.44 - 1.56: 7376 1.56 - 1.69: 24 1.69 - 1.81: 120 Bond restraints: 12736 Sorted by residual: bond pdb=" C21 POV A 401 " pdb=" O21 POV A 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C21 POV H 401 " pdb=" O21 POV H 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C21 POV F 401 " pdb=" O21 POV F 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C21 POV B 401 " pdb=" O21 POV B 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C21 POV G 401 " pdb=" O21 POV G 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 ... (remaining 12731 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.49: 488 106.49 - 113.35: 7064 113.35 - 120.21: 4712 120.21 - 127.08: 4976 127.08 - 133.94: 168 Bond angle restraints: 17408 Sorted by residual: angle pdb=" C13 POV H 401 " pdb=" N POV H 401 " pdb=" C14 POV H 401 " ideal model delta sigma weight residual 108.80 128.17 -19.37 3.00e+00 1.11e-01 4.17e+01 angle pdb=" C13 POV A 401 " pdb=" N POV A 401 " pdb=" C14 POV A 401 " ideal model delta sigma weight residual 108.80 128.17 -19.37 3.00e+00 1.11e-01 4.17e+01 angle pdb=" C13 POV D 401 " pdb=" N POV D 401 " pdb=" C14 POV D 401 " ideal model delta sigma weight residual 108.80 128.16 -19.36 3.00e+00 1.11e-01 4.17e+01 angle pdb=" C13 POV E 401 " pdb=" N POV E 401 " pdb=" C14 POV E 401 " ideal model delta sigma weight residual 108.80 128.16 -19.36 3.00e+00 1.11e-01 4.16e+01 angle pdb=" C13 POV G 401 " pdb=" N POV G 401 " pdb=" C14 POV G 401 " ideal model delta sigma weight residual 108.80 128.16 -19.36 3.00e+00 1.11e-01 4.16e+01 ... (remaining 17403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 7024 22.84 - 45.68: 471 45.68 - 68.52: 81 68.52 - 91.36: 24 91.36 - 114.20: 8 Dihedral angle restraints: 7608 sinusoidal: 2568 harmonic: 5040 Sorted by residual: dihedral pdb=" CA VAL D 159 " pdb=" C VAL D 159 " pdb=" N PRO D 160 " pdb=" CA PRO D 160 " ideal model delta harmonic sigma weight residual 180.00 151.48 28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA VAL E 159 " pdb=" C VAL E 159 " pdb=" N PRO E 160 " pdb=" CA PRO E 160 " ideal model delta harmonic sigma weight residual 180.00 151.51 28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA VAL C 159 " pdb=" C VAL C 159 " pdb=" N PRO C 160 " pdb=" CA PRO C 160 " ideal model delta harmonic sigma weight residual 180.00 151.51 28.49 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 7605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1265 0.034 - 0.068: 593 0.068 - 0.102: 175 0.102 - 0.136: 43 0.136 - 0.170: 12 Chirality restraints: 2088 Sorted by residual: chirality pdb=" CB THR D 236 " pdb=" CA THR D 236 " pdb=" OG1 THR D 236 " pdb=" CG2 THR D 236 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CB THR C 236 " pdb=" CA THR C 236 " pdb=" OG1 THR C 236 " pdb=" CG2 THR C 236 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CB THR E 236 " pdb=" CA THR E 236 " pdb=" OG1 THR E 236 " pdb=" CG2 THR E 236 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.08e-01 ... (remaining 2085 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F 161 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO F 162 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO F 162 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 162 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS H 161 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO H 162 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO H 162 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 162 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 161 " 0.039 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO A 162 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 162 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 162 " 0.032 5.00e-02 4.00e+02 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 8 2.24 - 2.90: 5074 2.90 - 3.57: 17349 3.57 - 4.23: 24304 4.23 - 4.90: 39463 Nonbonded interactions: 86198 Sorted by model distance: nonbonded pdb=" CB ASN F 255 " pdb=" CE2 TYR H 219 " model vdw 1.574 3.740 nonbonded pdb=" CB ASN E 255 " pdb=" CE2 TYR G 219 " model vdw 1.574 3.740 nonbonded pdb=" CB ASN D 255 " pdb=" CE2 TYR F 219 " model vdw 1.575 3.740 nonbonded pdb=" CB ASN B 255 " pdb=" CE2 TYR C 219 " model vdw 1.575 3.740 nonbonded pdb=" CB ASN C 255 " pdb=" CE2 TYR E 219 " model vdw 1.575 3.740 ... (remaining 86193 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 2.290 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: 8.080 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 34.380 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.110 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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 : 0.006 0.090 12736 Z= 0.425 Angle : 1.181 19.371 17408 Z= 0.527 Chirality : 0.043 0.170 2088 Planarity : 0.006 0.058 2176 Dihedral : 16.940 114.197 4288 Min Nonbonded Distance : 1.574 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.56 % Favored : 86.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.54 (0.17), residues: 1664 helix: -3.40 (0.12), residues: 912 sheet: None (None), residues: 0 loop : -4.03 (0.22), residues: 752 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.378 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2726 time to fit residues: 84.6259 Evaluate side-chains 204 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.350 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12736 Z= 0.221 Angle : 0.791 10.480 17408 Z= 0.376 Chirality : 0.043 0.170 2088 Planarity : 0.006 0.046 2176 Dihedral : 13.056 109.154 2112 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.02 % Favored : 87.98 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -3.63 (0.20), residues: 1664 helix: -1.63 (0.15), residues: 1008 sheet: None (None), residues: 0 loop : -3.64 (0.24), residues: 656 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 210 time to evaluate : 1.331 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 212 average time/residue: 0.2172 time to fit residues: 68.1885 Evaluate side-chains 204 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1084 time to fit residues: 4.2591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 0.2980 chunk 126 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 52 optimal weight: 0.0870 chunk 122 optimal weight: 1.9990 overall best weight: 2.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN A 72 ASN C 72 ASN D 72 ASN E 72 ASN F 72 ASN G 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 12736 Z= 0.255 Angle : 0.793 10.943 17408 Z= 0.369 Chirality : 0.043 0.139 2088 Planarity : 0.005 0.046 2176 Dihedral : 12.571 109.630 2112 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.21), residues: 1664 helix: -1.11 (0.16), residues: 1008 sheet: None (None), residues: 0 loop : -3.66 (0.24), residues: 656 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 194 time to evaluate : 1.366 Fit side-chains outliers start: 25 outliers final: 11 residues processed: 215 average time/residue: 0.2329 time to fit residues: 72.7980 Evaluate side-chains 193 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 182 time to evaluate : 1.374 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1059 time to fit residues: 3.9938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 16 optimal weight: 0.0970 chunk 72 optimal weight: 0.5980 chunk 102 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN E 105 GLN G 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 12736 Z= 0.160 Angle : 0.715 10.369 17408 Z= 0.329 Chirality : 0.040 0.122 2088 Planarity : 0.005 0.047 2176 Dihedral : 11.337 106.322 2112 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer Outliers : 2.76 % 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: -2.40 (0.21), residues: 1664 helix: -0.57 (0.17), residues: 1016 sheet: None (None), residues: 0 loop : -3.31 (0.25), residues: 648 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 207 time to evaluate : 1.438 Fit side-chains outliers start: 30 outliers final: 8 residues processed: 225 average time/residue: 0.2462 time to fit residues: 78.7255 Evaluate side-chains 195 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 187 time to evaluate : 1.360 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1056 time to fit residues: 3.3311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 0.0070 chunk 138 optimal weight: 2.9990 chunk 112 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 ASN F 72 ASN G 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 12736 Z= 0.210 Angle : 0.778 10.725 17408 Z= 0.354 Chirality : 0.041 0.120 2088 Planarity : 0.005 0.046 2176 Dihedral : 11.283 109.042 2112 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer Outliers : 1.84 % 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: -2.09 (0.22), residues: 1664 helix: -0.29 (0.17), residues: 1016 sheet: None (None), residues: 0 loop : -3.24 (0.25), residues: 648 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 192 time to evaluate : 1.384 Fit side-chains outliers start: 20 outliers final: 7 residues processed: 204 average time/residue: 0.2340 time to fit residues: 69.9047 Evaluate side-chains 183 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 176 time to evaluate : 1.366 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1063 time to fit residues: 3.2109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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: 65.1726 > 50: distance: 42 - 67: 27.925 distance: 45 - 50: 17.676 distance: 46 - 72: 26.976 distance: 50 - 51: 17.176 distance: 51 - 52: 17.649 distance: 51 - 54: 15.468 distance: 52 - 53: 10.180 distance: 52 - 59: 4.137 distance: 53 - 83: 23.162 distance: 54 - 55: 21.339 distance: 55 - 56: 5.948 distance: 56 - 57: 15.918 distance: 56 - 58: 5.098 distance: 59 - 60: 10.553 distance: 60 - 61: 32.177 distance: 60 - 63: 9.111 distance: 61 - 62: 12.264 distance: 61 - 67: 18.001 distance: 62 - 91: 43.912 distance: 63 - 64: 15.520 distance: 64 - 65: 21.764 distance: 64 - 66: 12.000 distance: 67 - 68: 8.551 distance: 68 - 69: 30.575 distance: 68 - 71: 8.780 distance: 69 - 70: 16.108 distance: 69 - 72: 31.467 distance: 70 - 99: 46.912 distance: 72 - 73: 16.151 distance: 73 - 74: 12.023 distance: 73 - 76: 15.008 distance: 74 - 75: 26.759 distance: 74 - 83: 25.410 distance: 76 - 77: 27.430 distance: 77 - 78: 17.828 distance: 78 - 79: 10.691 distance: 79 - 80: 11.319 distance: 80 - 81: 10.238 distance: 80 - 82: 5.830 distance: 83 - 84: 30.106 distance: 84 - 85: 55.925 distance: 84 - 87: 17.565 distance: 85 - 86: 48.987 distance: 85 - 91: 53.212 distance: 87 - 88: 28.272 distance: 88 - 89: 15.815 distance: 88 - 90: 7.060 distance: 91 - 92: 20.695 distance: 92 - 93: 8.984 distance: 92 - 95: 17.137 distance: 93 - 94: 25.996 distance: 93 - 99: 24.923 distance: 95 - 96: 16.552 distance: 96 - 98: 25.644 distance: 99 - 100: 13.344 distance: 100 - 101: 9.850 distance: 100 - 103: 38.870 distance: 101 - 102: 28.139 distance: 101 - 104: 20.636 distance: 105 - 106: 7.407 distance: 105 - 108: 8.421 distance: 106 - 107: 15.425 distance: 106 - 115: 3.191 distance: 108 - 109: 3.338 distance: 109 - 110: 17.433 distance: 111 - 112: 3.846 distance: 112 - 113: 24.370 distance: 112 - 114: 6.396 distance: 115 - 116: 19.468 distance: 116 - 117: 37.934 distance: 116 - 119: 6.418 distance: 117 - 122: 31.484 distance: 119 - 121: 25.752 distance: 122 - 123: 9.131 distance: 122 - 128: 54.078 distance: 123 - 124: 35.288 distance: 123 - 126: 51.810 distance: 124 - 129: 35.397 distance: 126 - 127: 38.149 distance: 127 - 128: 12.026