Starting phenix.real_space_refine on Mon Mar 11 13:14:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8o_24899/03_2024/7s8o_24899_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8o_24899/03_2024/7s8o_24899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8o_24899/03_2024/7s8o_24899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8o_24899/03_2024/7s8o_24899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8o_24899/03_2024/7s8o_24899_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8o_24899/03_2024/7s8o_24899_updated.pdb" } resolution = 2.58 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= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5332 2.51 5 N 1407 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 337": "OD1" <-> "OD2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3": "OE1" <-> "OE2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 206": "NH1" <-> "NH2" Residue "E TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8331 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1893 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain breaks: 1 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 9, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1707 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2564 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 401 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1743 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "R" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'8IU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.74, per 1000 atoms: 0.57 Number of scatterers: 8331 At special positions: 0 Unit cell: (91.91, 125.58, 121.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1530 8.00 N 1407 7.00 C 5332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " 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: 3.03 Conformation dependent library (CDL) restraints added in 1.5 seconds 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 12 sheets defined 33.3% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'R' and resid 31 through 56 removed outlier: 3.770A pdb=" N PHE R 35 " --> pdb=" O LEU R 31 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL R 43 " --> pdb=" O PHE R 39 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY R 44 " --> pdb=" O ILE R 40 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY R 47 " --> pdb=" O VAL R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 94 Processing helix chain 'R' and resid 103 through 132 removed outlier: 3.941A pdb=" N THR R 107 " --> pdb=" O SER R 103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU R 120 " --> pdb=" O GLY R 116 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 Processing helix chain 'R' and resid 145 through 168 removed outlier: 3.715A pdb=" N PHE R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 211 Processing helix chain 'R' and resid 218 through 235 Processing helix chain 'R' and resid 237 through 249 removed outlier: 5.279A pdb=" N LEU R 247 " --> pdb=" O TRP R 243 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TRP R 248 " --> pdb=" O PHE R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 280 removed outlier: 4.065A pdb=" N ILE R 260 " --> pdb=" O LEU R 256 " (cutoff:3.500A) Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'B' and resid 7 through 32 removed outlier: 4.128A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 212 through 215 removed outlier: 3.619A pdb=" N PHE B 215 " --> pdb=" O ILE B 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 212 through 215' Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 296 through 310 removed outlier: 4.211A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 349 removed outlier: 3.944A pdb=" N ASP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 23 removed outlier: 3.510A pdb=" N LEU C 14 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'D' and resid 9 through 22 Processing helix chain 'D' and resid 30 through 44 removed outlier: 3.528A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 319 through 323 removed outlier: 6.611A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.033A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.990A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.938A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.935A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.674A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.665A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 46 through 51 removed outlier: 3.954A pdb=" N ARG C 46 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.540A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 143 through 148 Processing sheet with id= L, first strand: chain 'E' and resid 214 through 219 removed outlier: 3.614A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 377 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2664 1.34 - 1.46: 1953 1.46 - 1.58: 3804 1.58 - 1.70: 1 1.70 - 1.81: 86 Bond restraints: 8508 Sorted by residual: bond pdb=" C03 8IU R 401 " pdb=" C04 8IU R 401 " ideal model delta sigma weight residual 1.528 1.320 0.208 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C04 8IU R 401 " pdb=" N05 8IU R 401 " ideal model delta sigma weight residual 1.457 1.647 -0.190 2.00e-02 2.50e+03 9.07e+01 bond pdb=" C21 8IU R 401 " pdb=" N05 8IU R 401 " ideal model delta sigma weight residual 1.470 1.326 0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" C03 8IU R 401 " pdb=" N02 8IU R 401 " ideal model delta sigma weight residual 1.448 1.557 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" N19 8IU R 401 " pdb=" N20 8IU R 401 " ideal model delta sigma weight residual 1.341 1.444 -0.103 2.00e-02 2.50e+03 2.63e+01 ... (remaining 8503 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.02: 120 106.02 - 113.03: 4642 113.03 - 120.03: 2861 120.03 - 127.04: 3839 127.04 - 134.04: 99 Bond angle restraints: 11561 Sorted by residual: angle pdb=" CA LEU R 163 " pdb=" C LEU R 163 " pdb=" N GLU R 164 " ideal model delta sigma weight residual 118.14 122.91 -4.77 1.31e+00 5.83e-01 1.32e+01 angle pdb=" N LEU R 237 " pdb=" CA LEU R 237 " pdb=" C LEU R 237 " ideal model delta sigma weight residual 109.81 117.45 -7.64 2.21e+00 2.05e-01 1.19e+01 angle pdb=" N PRO E 224 " pdb=" CA PRO E 224 " pdb=" C PRO E 224 " ideal model delta sigma weight residual 112.10 120.22 -8.12 2.60e+00 1.48e-01 9.74e+00 angle pdb=" CA TYR E 178 " pdb=" CB TYR E 178 " pdb=" CG TYR E 178 " ideal model delta sigma weight residual 113.90 119.47 -5.57 1.80e+00 3.09e-01 9.56e+00 angle pdb=" CA LEU B 227 " pdb=" CB LEU B 227 " pdb=" CG LEU B 227 " ideal model delta sigma weight residual 116.30 127.06 -10.76 3.50e+00 8.16e-02 9.45e+00 ... (remaining 11556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 4521 16.88 - 33.76: 364 33.76 - 50.64: 76 50.64 - 67.51: 18 67.51 - 84.39: 7 Dihedral angle restraints: 4986 sinusoidal: 1811 harmonic: 3175 Sorted by residual: dihedral pdb=" CA ARG E 206 " pdb=" C ARG E 206 " pdb=" N LEU E 207 " pdb=" CA LEU E 207 " ideal model delta harmonic sigma weight residual -180.00 -157.85 -22.15 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ASN B 347 " pdb=" C ASN B 347 " pdb=" N LEU B 348 " pdb=" CA LEU B 348 " ideal model delta harmonic sigma weight residual 180.00 158.06 21.94 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA CYS R 95 " pdb=" C CYS R 95 " pdb=" N SER R 96 " pdb=" CA SER R 96 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 4983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 863 0.038 - 0.076: 352 0.076 - 0.113: 96 0.113 - 0.151: 29 0.151 - 0.189: 3 Chirality restraints: 1343 Sorted by residual: chirality pdb=" CA PRO E 224 " pdb=" N PRO E 224 " pdb=" C PRO E 224 " pdb=" CB PRO E 224 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.93e-01 chirality pdb=" CA LEU R 237 " pdb=" N LEU R 237 " pdb=" C LEU R 237 " pdb=" CB LEU R 237 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CA ASN B 347 " pdb=" N ASN B 347 " pdb=" C ASN B 347 " pdb=" CB ASN B 347 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 1340 not shown) Planarity restraints: 1449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 135 " 0.044 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO E 136 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 136 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 136 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN R 242 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.94e+00 pdb=" C GLN R 242 " -0.034 2.00e-02 2.50e+03 pdb=" O GLN R 242 " 0.013 2.00e-02 2.50e+03 pdb=" N TRP R 243 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 123 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C VAL R 123 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL R 123 " 0.013 2.00e-02 2.50e+03 pdb=" N SER R 124 " 0.011 2.00e-02 2.50e+03 ... (remaining 1446 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 67 2.66 - 3.22: 7187 3.22 - 3.78: 11703 3.78 - 4.34: 15860 4.34 - 4.90: 28188 Nonbonded interactions: 63005 Sorted by model distance: nonbonded pdb=" OD1 ASP R 75 " pdb=" OG SER R 272 " model vdw 2.102 2.440 nonbonded pdb=" OG1 THR C 128 " pdb=" O GLU C 130 " model vdw 2.213 2.440 nonbonded pdb=" OH TYR R 113 " pdb=" O GLY R 236 " model vdw 2.259 2.440 nonbonded pdb=" O ASP C 333 " pdb=" OG SER C 334 " model vdw 2.310 2.440 nonbonded pdb=" O SER E 106 " pdb=" OG SER E 106 " model vdw 2.334 2.440 ... (remaining 63000 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 3.780 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.030 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:12.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.007 0.208 8508 Z= 0.586 Angle : 0.718 10.761 11561 Z= 0.386 Chirality : 0.046 0.189 1343 Planarity : 0.005 0.068 1449 Dihedral : 13.522 84.393 2935 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.31 (0.26), residues: 1083 helix: 2.11 (0.28), residues: 359 sheet: 0.95 (0.31), residues: 292 loop : -2.12 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 82 HIS 0.005 0.001 HIS C 91 PHE 0.020 0.002 PHE R 232 TYR 0.029 0.002 TYR E 178 ARG 0.007 0.001 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.846 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 1.1455 time to fit residues: 197.5039 Evaluate side-chains 148 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.5980 chunk 81 optimal weight: 0.0570 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 0.0020 chunk 32 optimal weight: 0.0030 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 155 ASN C 176 GLN C 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8508 Z= 0.121 Angle : 0.485 6.357 11561 Z= 0.256 Chirality : 0.040 0.133 1343 Planarity : 0.004 0.045 1449 Dihedral : 4.742 42.636 1193 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.27 % Allowed : 9.00 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.86 (0.26), residues: 1083 helix: 2.98 (0.28), residues: 356 sheet: 1.18 (0.32), residues: 273 loop : -1.98 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 248 HIS 0.002 0.001 HIS B 244 PHE 0.011 0.001 PHE R 104 TYR 0.009 0.001 TYR E 178 ARG 0.003 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 156 time to evaluate : 1.020 Fit side-chains REVERT: C 57 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8047 (ptmt) REVERT: C 217 MET cc_start: 0.7278 (pmt) cc_final: 0.6909 (pmt) outliers start: 11 outliers final: 2 residues processed: 161 average time/residue: 1.1505 time to fit residues: 197.4562 Evaluate side-chains 154 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 57 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 80 optimal weight: 0.0270 chunk 66 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 86 optimal weight: 0.0670 chunk 96 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 48 ASN B 22 ASN C 75 GLN C 132 ASN C 176 GLN C 340 ASN E 130 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8508 Z= 0.151 Angle : 0.498 6.573 11561 Z= 0.263 Chirality : 0.040 0.148 1343 Planarity : 0.003 0.038 1449 Dihedral : 4.246 23.363 1193 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.73 % Allowed : 13.38 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.01 (0.26), residues: 1083 helix: 3.18 (0.28), residues: 356 sheet: 1.26 (0.32), residues: 267 loop : -1.90 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 248 HIS 0.003 0.001 HIS B 244 PHE 0.012 0.001 PHE B 189 TYR 0.018 0.001 TYR E 178 ARG 0.002 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 153 time to evaluate : 1.016 Fit side-chains REVERT: C 57 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8018 (ptmt) REVERT: E 6 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8231 (pm20) REVERT: E 93 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7621 (ttp) outliers start: 15 outliers final: 5 residues processed: 161 average time/residue: 1.1654 time to fit residues: 199.9221 Evaluate side-chains 159 residues out of total 946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 54.462 > 50: distance: 25 - 115: 4.880 distance: 35 - 101: 9.999 distance: 38 - 98: 5.939 distance: 79 - 109: 8.951 distance: 82 - 106: 5.058 distance: 99 - 100: 5.390 distance: 99 - 102: 4.440 distance: 100 - 101: 8.996 distance: 100 - 106: 3.480 distance: 103 - 105: 8.421 distance: 106 - 107: 6.052 distance: 107 - 110: 3.659 distance: 108 - 109: 5.897 distance: 108 - 115: 5.455 distance: 110 - 111: 6.340 distance: 111 - 112: 6.367 distance: 112 - 113: 4.618 distance: 112 - 114: 10.275 distance: 115 - 116: 10.118 distance: 116 - 117: 7.151 distance: 116 - 119: 4.011 distance: 117 - 118: 3.452 distance: 119 - 120: 6.788 distance: 121 - 122: 16.860 distance: 123 - 124: 5.794 distance: 124 - 125: 6.719 distance: 124 - 127: 4.783 distance: 125 - 126: 14.595 distance: 125 - 130: 16.504 distance: 127 - 128: 9.564 distance: 127 - 129: 10.854 distance: 130 - 131: 12.168 distance: 131 - 132: 21.031 distance: 131 - 134: 20.628 distance: 132 - 133: 18.736 distance: 132 - 136: 7.091 distance: 134 - 135: 17.681 distance: 136 - 137: 11.424 distance: 137 - 138: 8.772 distance: 137 - 140: 8.336 distance: 138 - 139: 16.135 distance: 138 - 144: 7.266 distance: 140 - 141: 8.671 distance: 141 - 142: 6.993 distance: 141 - 143: 6.955 distance: 144 - 145: 13.827 distance: 145 - 146: 9.540 distance: 145 - 148: 6.691 distance: 146 - 147: 10.575 distance: 146 - 155: 14.077 distance: 149 - 150: 7.497 distance: 150 - 151: 5.736 distance: 151 - 152: 8.241 distance: 152 - 153: 10.477 distance: 152 - 154: 10.854 distance: 155 - 156: 13.941 distance: 156 - 157: 7.159 distance: 156 - 159: 27.166 distance: 157 - 158: 23.879 distance: 157 - 161: 4.988 distance: 159 - 160: 22.561 distance: 161 - 162: 8.932 distance: 162 - 163: 10.217 distance: 162 - 165: 12.263 distance: 163 - 164: 8.289 distance: 163 - 166: 5.222 distance: 166 - 167: 6.956 distance: 167 - 168: 3.069 distance: 167 - 170: 6.953 distance: 168 - 169: 4.706 distance: 168 - 174: 3.735 distance: 170 - 171: 10.773 distance: 171 - 172: 9.953