Starting phenix.real_space_refine on Sun Mar 17 04:57:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8so3_40646/03_2024/8so3_40646_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8so3_40646/03_2024/8so3_40646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8so3_40646/03_2024/8so3_40646.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8so3_40646/03_2024/8so3_40646.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8so3_40646/03_2024/8so3_40646_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8so3_40646/03_2024/8so3_40646_trim.pdb" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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 S 34 5.16 5 C 5517 2.51 5 N 1509 2.21 5 O 1711 1.98 5 H 7947 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L GLU 165": "OE1" <-> "OE2" Residue "Y GLU 46": "OE1" <-> "OE2" Residue "Y PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z GLU 109": "OE1" <-> "OE2" Residue "Z GLU 199": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16718 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2308 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 19, 'TRANS': 153} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 90 Chain: "H" Number of atoms: 3005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3005 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3010 Classifications: {'peptide': 216} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 202} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "X" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 2279 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 19, 'TRANS': 155} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 127 Chain: "Y" Number of atoms: 3035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3035 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Z" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3025 Classifications: {'peptide': 216} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 202} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.58, per 1000 atoms: 0.45 Number of scatterers: 16718 At special positions: 0 Unit cell: (96.32, 100.8, 128.8, 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 34 16.00 O 1711 8.00 N 1509 7.00 C 5517 6.00 H 7947 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS D 44 " - pdb=" SG CYS D 160 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 241 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS X 44 " - pdb=" SG CYS X 160 " distance=2.03 Simple disulfide: pdb=" SG CYS X 189 " - pdb=" SG CYS X 241 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 144 " - pdb=" SG CYS Y 200 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 138 " - pdb=" SG CYS Z 198 " 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: 12.77 Conformation dependent library (CDL) restraints added in 2.0 seconds 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 31 sheets defined 5.9% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'D' and resid 206 through 210 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.205A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 189 through 193 removed outlier: 3.588A pdb=" N LEU H 193 " --> pdb=" O SER H 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 67 removed outlier: 3.513A pdb=" N PHE L 66 " --> pdb=" O PRO L 63 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER L 67 " --> pdb=" O ALA L 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 63 through 67' Processing helix chain 'L' and resid 125 through 132 removed outlier: 3.554A pdb=" N LEU L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 193 removed outlier: 3.987A pdb=" N HIS L 193 " --> pdb=" O ASP L 189 " (cutoff:3.500A) Processing helix chain 'X' and resid 232 through 236 Processing helix chain 'Y' and resid 28 through 32 removed outlier: 3.553A pdb=" N ASP Y 31 " --> pdb=" O THR Y 28 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR Y 32 " --> pdb=" O PHE Y 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 28 through 32' Processing helix chain 'Y' and resid 160 through 162 No H-bonds generated for 'chain 'Y' and resid 160 through 162' Processing helix chain 'Y' and resid 189 through 195 removed outlier: 3.631A pdb=" N LEU Y 193 " --> pdb=" O SER Y 190 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY Y 194 " --> pdb=" O SER Y 191 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 131 removed outlier: 3.650A pdb=" N SER Z 131 " --> pdb=" O GLU Z 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 192 Processing sheet with id=AA1, first strand: chain 'D' and resid 41 through 42 Processing sheet with id=AA2, first strand: chain 'D' and resid 99 through 103 removed outlier: 3.686A pdb=" N TYR D 99 " --> pdb=" O HIS D 65 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N TRP D 63 " --> pdb=" O VAL D 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 185 through 187 removed outlier: 3.548A pdb=" N LEU D 226 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 199 through 203 removed outlier: 3.882A pdb=" N GLY D 240 " --> pdb=" O PHE D 203 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP D 239 " --> pdb=" O TYR D 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.851A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.851A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR H 100 " --> pdb=" O MET H 106 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N MET H 106 " --> pdb=" O TYR H 100 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 124 through 128 removed outlier: 3.646A pdb=" N SER H 124 " --> pdb=" O LYS H 147 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS H 147 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE H 126 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU H 145 " --> pdb=" O PHE H 126 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 124 through 128 removed outlier: 3.646A pdb=" N SER H 124 " --> pdb=" O LYS H 147 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS H 147 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE H 126 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU H 145 " --> pdb=" O PHE H 126 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER H 181 " --> pdb=" O VAL H 173 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 154 through 158 removed outlier: 3.541A pdb=" N THR H 155 " --> pdb=" O ASN H 203 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS H 213 " --> pdb=" O CYS H 200 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.703A pdb=" N CYS L 23 " --> pdb=" O PHE L 75 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE L 75 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 19 through 20 Processing sheet with id=AB4, first strand: chain 'L' and resid 57 through 58 removed outlier: 6.223A pdb=" N LEU L 50 " --> pdb=" O GLN L 41 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLN L 41 " --> pdb=" O LEU L 50 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE L 52 " --> pdb=" O TRP L 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 118 through 122 removed outlier: 3.947A pdb=" N VAL L 137 " --> pdb=" O PHE L 122 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR L 177 " --> pdb=" O ASN L 142 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER L 180 " --> pdb=" O SER L 166 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER L 166 " --> pdb=" O SER L 180 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 149 through 154 removed outlier: 3.515A pdb=" N LYS L 149 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU L 199 " --> pdb=" O GLN L 151 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL L 200 " --> pdb=" O VAL L 209 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL L 209 " --> pdb=" O VAL L 200 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 40 through 43 Processing sheet with id=AB8, first strand: chain 'X' and resid 99 through 100 Processing sheet with id=AB9, first strand: chain 'X' and resid 172 through 173 removed outlier: 3.748A pdb=" N ASN X 188 " --> pdb=" O THR X 172 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU X 187 " --> pdb=" O LEU X 226 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU X 226 " --> pdb=" O LEU X 187 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS X 220 " --> pdb=" O PHE X 227 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 199 through 203 Processing sheet with id=AC2, first strand: chain 'Y' and resid 3 through 4 removed outlier: 3.794A pdb=" N LEU Y 3 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER Y 25 " --> pdb=" O LEU Y 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'Y' and resid 10 through 12 removed outlier: 3.915A pdb=" N GLU Y 10 " --> pdb=" O SER Y 114 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR Y 116 " --> pdb=" O GLU Y 10 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL Y 12 " --> pdb=" O THR Y 116 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL Y 34 " --> pdb=" O ASP Y 50 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASP Y 50 " --> pdb=" O VAL Y 34 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP Y 36 " --> pdb=" O ILE Y 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Y' and resid 10 through 12 removed outlier: 3.915A pdb=" N GLU Y 10 " --> pdb=" O SER Y 114 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR Y 116 " --> pdb=" O GLU Y 10 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL Y 12 " --> pdb=" O THR Y 116 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Y' and resid 19 through 21 Processing sheet with id=AC6, first strand: chain 'Y' and resid 124 through 128 removed outlier: 3.559A pdb=" N GLY Y 143 " --> pdb=" O LEU Y 128 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ALA Y 141 " --> pdb=" O VAL Y 188 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL Y 188 " --> pdb=" O ALA Y 141 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY Y 143 " --> pdb=" O VAL Y 186 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL Y 186 " --> pdb=" O GLY Y 143 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU Y 145 " --> pdb=" O SER Y 184 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER Y 184 " --> pdb=" O LEU Y 145 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS Y 147 " --> pdb=" O LEU Y 182 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU Y 182 " --> pdb=" O LYS Y 147 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL Y 185 " --> pdb=" O HIS Y 168 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Y' and resid 124 through 128 removed outlier: 3.559A pdb=" N GLY Y 143 " --> pdb=" O LEU Y 128 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ALA Y 141 " --> pdb=" O VAL Y 188 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL Y 188 " --> pdb=" O ALA Y 141 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY Y 143 " --> pdb=" O VAL Y 186 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL Y 186 " --> pdb=" O GLY Y 143 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU Y 145 " --> pdb=" O SER Y 184 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER Y 184 " --> pdb=" O LEU Y 145 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS Y 147 " --> pdb=" O LEU Y 182 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU Y 182 " --> pdb=" O LYS Y 147 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL Y 173 " --> pdb=" O SER Y 181 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Y' and resid 155 through 158 removed outlier: 4.606A pdb=" N TYR Y 198 " --> pdb=" O VAL Y 215 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS Y 213 " --> pdb=" O CYS Y 200 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL Y 211 " --> pdb=" O VAL Y 202 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Z' and resid 4 through 5 Processing sheet with id=AD1, first strand: chain 'Z' and resid 10 through 12 removed outlier: 6.788A pdb=" N LEU Z 11 " --> pdb=" O GLU Z 109 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET Z 37 " --> pdb=" O SER Z 53 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER Z 53 " --> pdb=" O MET Z 37 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TRP Z 39 " --> pdb=" O LEU Z 51 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU Z 51 " --> pdb=" O TRP Z 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Z' and resid 19 through 20 Processing sheet with id=AD3, first strand: chain 'Z' and resid 118 through 122 removed outlier: 3.662A pdb=" N VAL Z 137 " --> pdb=" O PHE Z 122 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR Z 177 " --> pdb=" O ASN Z 142 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Z' and resid 148 through 154 removed outlier: 3.974A pdb=" N TYR Z 196 " --> pdb=" O PHE Z 213 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE Z 213 " --> pdb=" O TYR Z 196 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 609 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.69 Time building geometry restraints manager: 13.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 7947 1.04 - 1.23: 389 1.23 - 1.43: 3482 1.43 - 1.63: 5080 1.63 - 1.82: 44 Bond restraints: 16942 Sorted by residual: bond pdb=" N THR Y 120 " pdb=" CA THR Y 120 " ideal model delta sigma weight residual 1.463 1.516 -0.053 1.24e-02 6.50e+03 1.80e+01 bond pdb=" NZ LYS Z 24 " pdb=" HZ1 LYS Z 24 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS H 63 " pdb=" HZ1 LYS H 63 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS Y 38 " pdb=" HZ2 LYS Y 38 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS Z 211 " pdb=" HZ1 LYS Z 211 " ideal model delta sigma weight residual 0.890 0.970 -0.080 2.00e-02 2.50e+03 1.62e+01 ... (remaining 16937 not shown) Histogram of bond angle deviations from ideal: 86.74 - 101.88: 21 101.88 - 117.03: 21879 117.03 - 132.18: 8457 132.18 - 147.33: 28 147.33 - 162.47: 2 Bond angle restraints: 30387 Sorted by residual: angle pdb=" CA GLY D 130 " pdb=" N GLY D 130 " pdb=" H GLY D 130 " ideal model delta sigma weight residual 114.00 162.47 -48.47 3.00e+00 1.11e-01 2.61e+02 angle pdb=" CA ASP X 131 " pdb=" N ASP X 131 " pdb=" H ASP X 131 " ideal model delta sigma weight residual 114.00 159.67 -45.67 3.00e+00 1.11e-01 2.32e+02 angle pdb=" C ARG D 165 " pdb=" N LEU D 166 " pdb=" CA LEU D 166 " ideal model delta sigma weight residual 120.90 136.32 -15.42 1.41e+00 5.03e-01 1.20e+02 angle pdb=" CA GLY D 60 " pdb=" N GLY D 60 " pdb=" H GLY D 60 " ideal model delta sigma weight residual 114.00 141.42 -27.42 3.00e+00 1.11e-01 8.35e+01 angle pdb=" CA GLY D 93 " pdb=" N GLY D 93 " pdb=" H GLY D 93 " ideal model delta sigma weight residual 114.00 86.74 27.26 3.00e+00 1.11e-01 8.26e+01 ... (remaining 30382 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7605 17.97 - 35.94: 524 35.94 - 53.91: 173 53.91 - 71.88: 39 71.88 - 89.85: 13 Dihedral angle restraints: 8354 sinusoidal: 4305 harmonic: 4049 Sorted by residual: dihedral pdb=" CB CYS Z 23 " pdb=" SG CYS Z 23 " pdb=" SG CYS Z 92 " pdb=" CB CYS Z 92 " ideal model delta sinusoidal sigma weight residual 93.00 165.95 -72.95 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS Y 144 " pdb=" SG CYS Y 144 " pdb=" SG CYS Y 200 " pdb=" CB CYS Y 200 " ideal model delta sinusoidal sigma weight residual 93.00 142.20 -49.20 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" CA ARG D 165 " pdb=" C ARG D 165 " pdb=" N LEU D 166 " pdb=" CA LEU D 166 " ideal model delta harmonic sigma weight residual -180.00 -152.49 -27.51 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 8351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1204 0.068 - 0.136: 186 0.136 - 0.204: 13 0.204 - 0.272: 3 0.272 - 0.340: 1 Chirality restraints: 1407 Sorted by residual: chirality pdb=" CA ARG D 165 " pdb=" N ARG D 165 " pdb=" C ARG D 165 " pdb=" CB ARG D 165 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA MET X 171 " pdb=" N MET X 171 " pdb=" C MET X 171 " pdb=" CB MET X 171 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA LYS H 38 " pdb=" N LYS H 38 " pdb=" C LYS H 38 " pdb=" CB LYS H 38 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1404 not shown) Planarity restraints: 2697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER X 69 " -0.023 2.00e-02 2.50e+03 4.63e-02 2.15e+01 pdb=" C SER X 69 " 0.080 2.00e-02 2.50e+03 pdb=" O SER X 69 " -0.030 2.00e-02 2.50e+03 pdb=" N GLY X 70 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 163 " 0.020 2.00e-02 2.50e+03 4.21e-02 1.78e+01 pdb=" C ARG D 163 " -0.073 2.00e-02 2.50e+03 pdb=" O ARG D 163 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU D 164 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 165 " -0.018 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C ARG D 165 " 0.067 2.00e-02 2.50e+03 pdb=" O ARG D 165 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU D 166 " -0.023 2.00e-02 2.50e+03 ... (remaining 2694 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.87: 77 1.87 - 2.55: 14520 2.55 - 3.24: 46250 3.24 - 3.92: 58238 3.92 - 4.60: 90498 Nonbonded interactions: 209583 Sorted by model distance: nonbonded pdb=" H TYR X 147 " pdb=" HA ARG X 163 " model vdw 1.188 2.270 nonbonded pdb=" HE3 MET X 171 " pdb=" HB2 CYS X 241 " model vdw 1.276 2.440 nonbonded pdb=" HG3 GLU X 146 " pdb=" CB ARG X 163 " model vdw 1.315 2.920 nonbonded pdb=" HA GLU X 146 " pdb=" O ARG X 163 " model vdw 1.327 2.620 nonbonded pdb=" HE2 TYR X 255 " pdb="HD21 LEU X 257 " model vdw 1.330 2.270 ... (remaining 209578 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 'D' and (resid 27 or (resid 28 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 29 through 71 or (resid 72 and (nam \ e N or name CA or name C or name O or name CB or name HA )) or resid 93 through \ 104 or (resid 131 through 132 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 133 through 134 or (resid 135 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 136 th \ rough 157 or (resid 158 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 159 through 167 or (resid 168 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 169 through \ 203 or (resid 204 through 206 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 207 through 214 or (resid 215 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 216 th \ rough 222 or (resid 223 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 224 through 257 or resid 601)) selection = (chain 'X' and (resid 27 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 37 through 72 or resid 9 \ 3 through 137 or (resid 138 and (name N or name CA or name C or name O or name C \ B or name HA )) or resid 139 through 178 or (resid 179 through 180 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 181 th \ rough 229 or (resid 230 through 232 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 233 through 252 or (resid 253 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 254 through 257 or resid 601)) } ncs_group { reference = (chain 'H' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 4 or (resid 5 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 6 through 9 or ( \ resid 10 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 11 through 24 or (resid 25 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 26 through 85 or (resid 86 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 87 through 217 or (resid 218 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 219)) selection = (chain 'Y' and (resid 2 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 14 through 17 or (resid 1 \ 8 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 19 through 29 or (resid 30 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 31 through 40 or (resid 41 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 42 \ through 61 or (resid 62 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 63 through 64 or (resid 65 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 66 through 68 o \ r (resid 69 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 70 through 88 or (resid 89 through 90 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 91 through 219)) \ } ncs_group { reference = (chain 'L' and (resid 1 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 35 through 84 or (resid 8 \ 5 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 86 through 216)) selection = (chain 'Z' and (resid 1 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 28 through 45 or (resid 4 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 through 96 or (resid 97 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 98 through 216)) } 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=0.00 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: 3.770 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: 0.270 Extract box with map and model: 7.650 Check model and map are aligned: 0.430 Set scattering table: 0.300 Process input model: 53.760 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 0.087 8995 Z= 0.308 Angle : 0.852 16.221 12316 Z= 0.496 Chirality : 0.051 0.340 1407 Planarity : 0.007 0.065 1598 Dihedral : 13.957 89.848 3097 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.46 % Favored : 93.37 % Rotamer: Outliers : 0.68 % Allowed : 0.90 % Favored : 98.42 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 12.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.24), residues: 1177 helix: -0.48 (0.83), residues: 34 sheet: -0.53 (0.24), residues: 479 loop : -1.37 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 109 HIS 0.013 0.001 HIS X 65 PHE 0.016 0.002 PHE L 75 TYR 0.014 0.001 TYR D 245 ARG 0.017 0.001 ARG D 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 1.346 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR L 76 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR Z 76 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: D 166 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8365 (tt) REVERT: X 32 VAL cc_start: 0.8175 (p) cc_final: 0.7837 (m) REVERT: X 161 ARG cc_start: 0.7799 (ttm110) cc_final: 0.7503 (ttm110) outliers start: 6 outliers final: 3 residues processed: 135 average time/residue: 0.4036 time to fit residues: 76.1355 Evaluate side-chains 108 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain X residue 162 LEU Chi-restraints excluded: chain X residue 172 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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: 68.9524 > 50: distance: 95 - 108: 18.215 distance: 108 - 109: 14.243 distance: 108 - 116: 9.186 distance: 109 - 110: 51.263 distance: 109 - 112: 22.056 distance: 109 - 117: 41.208 distance: 110 - 111: 41.135 distance: 110 - 127: 28.754 distance: 112 - 113: 9.715 distance: 112 - 114: 15.817 distance: 112 - 118: 11.811 distance: 113 - 115: 8.749 distance: 113 - 119: 23.993 distance: 113 - 120: 20.969 distance: 114 - 121: 11.518 distance: 114 - 122: 8.910 distance: 114 - 123: 13.225 distance: 115 - 124: 5.049 distance: 115 - 125: 11.716 distance: 115 - 126: 7.642 distance: 127 - 128: 31.818 distance: 127 - 136: 13.112 distance: 128 - 129: 6.715 distance: 128 - 131: 24.759 distance: 128 - 137: 26.372 distance: 129 - 130: 30.464 distance: 129 - 149: 12.749 distance: 131 - 132: 19.549 distance: 131 - 138: 16.910 distance: 131 - 139: 23.513 distance: 132 - 133: 8.235 distance: 132 - 140: 9.971 distance: 132 - 141: 4.155 distance: 133 - 134: 5.551 distance: 133 - 142: 8.103 distance: 133 - 143: 7.965 distance: 134 - 135: 18.464 distance: 134 - 144: 6.201 distance: 134 - 145: 5.326 distance: 135 - 146: 23.835 distance: 135 - 147: 17.295 distance: 135 - 148: 26.991 distance: 149 - 150: 20.977 distance: 149 - 154: 3.954 distance: 150 - 151: 32.123 distance: 150 - 153: 48.949 distance: 150 - 155: 42.023 distance: 151 - 152: 33.251 distance: 151 - 156: 40.579 distance: 156 - 157: 17.128 distance: 156 - 163: 18.844 distance: 157 - 158: 24.573 distance: 157 - 160: 19.076 distance: 157 - 164: 12.845 distance: 158 - 159: 13.137 distance: 158 - 170: 36.194 distance: 160 - 161: 5.974 distance: 160 - 162: 30.198 distance: 160 - 165: 43.493 distance: 161 - 166: 19.580 distance: 162 - 167: 21.458 distance: 162 - 168: 11.387 distance: 162 - 169: 11.245 distance: 170 - 171: 22.123 distance: 170 - 177: 40.291 distance: 171 - 172: 7.363 distance: 171 - 174: 16.883 distance: 171 - 178: 12.217 distance: 172 - 173: 28.828 distance: 172 - 186: 24.555 distance: 174 - 175: 11.736 distance: 174 - 176: 19.285 distance: 174 - 179: 23.730 distance: 175 - 180: 6.603 distance: 175 - 181: 14.227 distance: 175 - 182: 3.104 distance: 176 - 183: 25.201 distance: 176 - 184: 16.030 distance: 176 - 185: 21.188 distance: 186 - 187: 26.888 distance: 186 - 191: 29.402 distance: 187 - 188: 42.096 distance: 187 - 190: 26.291 distance: 187 - 192: 15.760 distance: 188 - 189: 5.994 distance: 188 - 196: 57.336 distance: 190 - 193: 32.831 distance: 190 - 194: 33.922 distance: 190 - 195: 22.892 distance: 196 - 197: 27.777 distance: 196 - 201: 39.539 distance: 197 - 198: 26.464 distance: 197 - 200: 32.394 distance: 197 - 202: 20.507 distance: 198 - 199: 32.720 distance: 198 - 206: 38.104 distance: 200 - 203: 45.162 distance: 200 - 204: 44.869 distance: 200 - 205: 40.368 distance: 206 - 207: 10.639 distance: 206 - 212: 39.851 distance: 207 - 208: 34.248 distance: 207 - 210: 30.184 distance: 207 - 213: 13.089 distance: 208 - 209: 39.073 distance: 208 - 220: 24.286 distance: 210 - 211: 41.565 distance: 210 - 214: 20.753 distance: 210 - 215: 48.259 distance: 211 - 212: 26.733 distance: 211 - 216: 36.769 distance: 211 - 217: 52.255 distance: 212 - 218: 27.319 distance: 212 - 219: 30.350 distance: 220 - 221: 23.021 distance: 220 - 226: 40.427 distance: 220 - 297: 30.807 distance: 221 - 222: 19.167 distance: 221 - 224: 27.091 distance: 221 - 227: 29.480 distance: 222 - 223: 38.696 distance: 222 - 231: 25.891 distance: 223 - 294: 30.647 distance: 224 - 225: 41.127 distance: 224 - 228: 45.161 distance: 224 - 229: 40.196 distance: 225 - 230: 36.019 distance: 231 - 232: 31.981 distance: 231 - 238: 51.757 distance: 232 - 233: 32.303 distance: 232 - 235: 27.946 distance: 232 - 239: 16.905 distance: 233 - 234: 28.598 distance: 233 - 247: 21.652 distance: 235 - 236: 29.576 distance: 235 - 237: 34.768 distance: 235 - 240: 33.892 distance: 236 - 241: 24.052 distance: 236 - 242: 19.021 distance: 236 - 243: 23.381 distance: 237 - 244: 30.887 distance: 237 - 245: 17.635 distance: 237 - 246: 10.086