Starting phenix.real_space_refine on Sun Mar 17 17:02:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzp_14393/03_2024/7yzp_14393_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzp_14393/03_2024/7yzp_14393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzp_14393/03_2024/7yzp_14393.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzp_14393/03_2024/7yzp_14393.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzp_14393/03_2024/7yzp_14393_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzp_14393/03_2024/7yzp_14393_updated.pdb" } resolution = 4.0 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4320 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 63 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 8650 2.51 5 N 2499 2.21 5 O 2851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 248": "OE1" <-> "OE2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 935": "OE1" <-> "OE2" Residue "C GLU 1018": "OE1" <-> "OE2" Residue "D GLU 180": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14107 Number of models: 1 Model: "" Number of chains: 9 Chain: "F" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1211 Classifications: {'DNA': 59} Link IDs: {'rna3p': 58} Chain: "A" Number of atoms: 3013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3013 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 20, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2819 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 20, 'TRANS': 335} Chain breaks: 4 Chain: "C" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3502 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 8, 'TRANS': 439} Chain breaks: 1 Chain: "D" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3502 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 8, 'TRANS': 439} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 21 residue: pdb=" N GLY A 284 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY A 284 " occ=0.50 residue: pdb=" N ALA A 287 " occ=0.60 ... (3 atoms not shown) pdb=" CB ALA A 287 " occ=0.60 residue: pdb=" N THR A 290 " occ=0.70 ... (5 atoms not shown) pdb=" CG2 THR A 290 " occ=0.70 residue: pdb=" N ALA A 291 " occ=0.60 ... (3 atoms not shown) pdb=" CB ALA A 291 " occ=0.60 residue: pdb=" N GLN A 292 " occ=0.70 ... (7 atoms not shown) pdb=" NE2 GLN A 292 " occ=0.70 residue: pdb=" N LEU A 293 " occ=0.80 ... (6 atoms not shown) pdb=" CD2 LEU A 293 " occ=0.80 residue: pdb=" N PRO A 303 " occ=0.61 ... (5 atoms not shown) pdb=" CD PRO A 303 " occ=0.61 residue: pdb=" N PRO A 304 " occ=0.68 ... (5 atoms not shown) pdb=" CD PRO A 304 " occ=0.68 residue: pdb=" N VAL A 305 " occ=0.88 ... (5 atoms not shown) pdb=" CG2 VAL A 305 " occ=0.88 residue: pdb=" N TRP A 306 " occ=0.97 ... (12 atoms not shown) pdb=" CH2 TRP A 306 " occ=0.97 residue: pdb=" N LEU A 307 " occ=0.87 ... (6 atoms not shown) pdb=" CD2 LEU A 307 " occ=0.87 residue: pdb=" N ILE A 309 " occ=0.89 ... (6 atoms not shown) pdb=" CD1 ILE A 309 " occ=0.89 ... (remaining 9 not shown) Time building chain proxies: 7.64, per 1000 atoms: 0.54 Number of scatterers: 14107 At special positions: 0 Unit cell: (100.605, 140.847, 139.788, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 38 16.00 P 63 15.00 Mg 2 11.99 O 2851 8.00 N 2499 7.00 C 8650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.39 Conformation dependent library (CDL) restraints added in 2.5 seconds 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 12 sheets defined 41.5% alpha, 13.9% beta 27 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 6.11 Creating SS restraints... Processing helix chain 'A' and resid 21 through 38 Processing helix chain 'A' and resid 57 through 73 removed outlier: 3.618A pdb=" N GLN A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 100 removed outlier: 4.450A pdb=" N SER A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N PHE A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 137 No H-bonds generated for 'chain 'A' and resid 134 through 137' Processing helix chain 'A' and resid 148 through 172 Processing helix chain 'A' and resid 286 through 297 removed outlier: 3.759A pdb=" N GLN A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N TRP A 296 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ARG A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 328 removed outlier: 3.848A pdb=" N GLN A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 362 through 372 removed outlier: 3.609A pdb=" N LEU A 372 " --> pdb=" O ARG A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 394 removed outlier: 4.180A pdb=" N ARG A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A 393 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 38 Processing helix chain 'B' and resid 57 through 73 removed outlier: 3.690A pdb=" N GLN B 72 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 99 removed outlier: 3.621A pdb=" N GLU B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N SER B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASP B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE B 96 " --> pdb=" O GLU B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 172 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.574A pdb=" N GLU B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TRP B 296 " --> pdb=" O GLN B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 328 removed outlier: 4.091A pdb=" N ARG B 322 " --> pdb=" O HIS B 318 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 327 " --> pdb=" O LYS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 362 through 372 removed outlier: 4.648A pdb=" N LEU B 372 " --> pdb=" O ARG B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 394 Processing helix chain 'C' and resid 45 through 55 removed outlier: 4.461A pdb=" N ILE C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 129 through 140 removed outlier: 4.247A pdb=" N GLU C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA C 137 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 150 removed outlier: 3.913A pdb=" N ARG C 149 " --> pdb=" O GLY C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 No H-bonds generated for 'chain 'C' and resid 160 through 163' Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 181 through 200 removed outlier: 3.691A pdb=" N PHE C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 215 through 234 removed outlier: 4.108A pdb=" N GLU C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS C 233 " --> pdb=" O THR C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 886 removed outlier: 3.588A pdb=" N GLN C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP C 879 " --> pdb=" O GLN C 875 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP C 880 " --> pdb=" O GLN C 876 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR C 882 " --> pdb=" O GLU C 878 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU C 883 " --> pdb=" O ASP C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 916 removed outlier: 3.908A pdb=" N GLY C 901 " --> pdb=" O LYS C 897 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 971 removed outlier: 3.982A pdb=" N VAL C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 988 No H-bonds generated for 'chain 'C' and resid 986 through 988' Processing helix chain 'C' and resid 991 through 1006 Processing helix chain 'C' and resid 1018 through 1023 Processing helix chain 'D' and resid 25 through 28 No H-bonds generated for 'chain 'D' and resid 25 through 28' Processing helix chain 'D' and resid 45 through 55 removed outlier: 4.908A pdb=" N ILE D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N CYS D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 144 through 150 removed outlier: 4.544A pdb=" N ARG D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 175 removed outlier: 4.292A pdb=" N GLU D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 209 removed outlier: 3.998A pdb=" N LEU D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 233 Processing helix chain 'D' and resid 836 through 887 removed outlier: 3.760A pdb=" N ARG D 840 " --> pdb=" O HIS D 836 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D 875 " --> pdb=" O ALA D 871 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN D 876 " --> pdb=" O GLN D 872 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP D 879 " --> pdb=" O GLN D 875 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU D 886 " --> pdb=" O TYR D 882 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 918 removed outlier: 4.733A pdb=" N LEU D 902 " --> pdb=" O PHE D 898 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN D 913 " --> pdb=" O HIS D 909 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 948 through 950 No H-bonds generated for 'chain 'D' and resid 948 through 950' Processing helix chain 'D' and resid 953 through 972 removed outlier: 3.762A pdb=" N VAL D 971 " --> pdb=" O LEU D 967 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER D 972 " --> pdb=" O SER D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 1005 removed outlier: 3.528A pdb=" N ASP D 995 " --> pdb=" O SER D 991 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N THR D 996 " --> pdb=" O GLU D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1018 through 1020 No H-bonds generated for 'chain 'D' and resid 1018 through 1020' Processing helix chain 'D' and resid 1043 through 1045 No H-bonds generated for 'chain 'D' and resid 1043 through 1045' Processing sheet with id= A, first strand: chain 'A' and resid 102 through 104 removed outlier: 6.208A pdb=" N LEU A 77 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 42 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 4 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 6 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 3 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER A 267 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER A 261 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 235 through 237 removed outlier: 6.808A pdb=" N ILE A 218 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU A 115 " --> pdb=" O GLY A 123 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 279 through 283 removed outlier: 6.556A pdb=" N TRP A 306 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEU A 282 " --> pdb=" O TRP A 306 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP A 308 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 336 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE A 309 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 264 through 271 removed outlier: 6.748A pdb=" N THR B 259 " --> pdb=" O GLU B 266 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 268 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU B 257 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN B 270 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL B 255 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS B 256 " --> pdb=" O HIS B 5 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ALA B 42 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N THR B 6 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 44 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N HIS B 76 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL B 45 " --> pdb=" O HIS B 76 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL B 78 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 235 through 237 removed outlier: 6.677A pdb=" N ILE B 218 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU B 115 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL B 125 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN B 113 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 279 through 284 removed outlier: 6.533A pdb=" N TRP B 306 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LEU B 282 " --> pdb=" O TRP B 306 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP B 308 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N GLY B 284 " --> pdb=" O ASP B 308 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU B 310 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE B 309 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL B 338 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE B 311 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG B 340 " --> pdb=" O ILE B 311 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 17 through 21 removed outlier: 4.066A pdb=" N GLU C 84 " --> pdb=" O SER C 5 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 80 " --> pdb=" O LYS C 9 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU C 115 " --> pdb=" O PHE C 95 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.580A pdb=" N PHE C 33 " --> pdb=" O ILE C1011 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 35 " --> pdb=" O VAL C1013 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU C 980 " --> pdb=" O THR C1010 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 922 through 926 Processing sheet with id= J, first strand: chain 'D' and resid 18 through 21 removed outlier: 6.556A pdb=" N GLU D 84 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU D 6 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU D 82 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU D 8 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU D 80 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 1039 through 1041 removed outlier: 7.611A pdb=" N ALA D 34 " --> pdb=" O ILE D1028 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N VAL D1030 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR D 36 " --> pdb=" O VAL D1030 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N LYS D1032 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 922 through 926 removed outlier: 3.510A pdb=" N ARG D 946 " --> pdb=" O VAL D 936 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1557 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 134 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 4.83 Time building geometry restraints manager: 6.77 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: 4471 1.34 - 1.46: 2318 1.46 - 1.58: 7491 1.58 - 1.70: 123 1.70 - 1.82: 60 Bond restraints: 14463 Sorted by residual: bond pdb=" C4 ADP D1101 " pdb=" C5 ADP D1101 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C4 ADP C1101 " pdb=" C5 ADP C1101 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C5 ADP D1101 " pdb=" C6 ADP D1101 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C5 ADP C1101 " pdb=" C6 ADP C1101 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" N ASP A 85 " pdb=" CA ASP A 85 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.14e-02 7.69e+03 9.25e+00 ... (remaining 14458 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.65: 703 106.65 - 113.61: 8092 113.61 - 120.57: 5797 120.57 - 127.53: 5063 127.53 - 134.49: 206 Bond angle restraints: 19861 Sorted by residual: angle pdb=" PA ADP D1101 " pdb=" O3A ADP D1101 " pdb=" PB ADP D1101 " ideal model delta sigma weight residual 120.50 134.49 -13.99 3.00e+00 1.11e-01 2.17e+01 angle pdb=" C ASN D 12 " pdb=" CA ASN D 12 " pdb=" CB ASN D 12 " ideal model delta sigma weight residual 116.63 111.67 4.96 1.16e+00 7.43e-01 1.83e+01 angle pdb=" N ASN A 83 " pdb=" CA ASN A 83 " pdb=" C ASN A 83 " ideal model delta sigma weight residual 113.12 107.86 5.26 1.25e+00 6.40e-01 1.77e+01 angle pdb=" N VAL C 971 " pdb=" CA VAL C 971 " pdb=" C VAL C 971 " ideal model delta sigma weight residual 112.29 108.37 3.92 9.40e-01 1.13e+00 1.74e+01 angle pdb=" PA ADP C1101 " pdb=" O3A ADP C1101 " pdb=" PB ADP C1101 " ideal model delta sigma weight residual 120.50 131.68 -11.18 3.00e+00 1.11e-01 1.39e+01 ... (remaining 19856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.90: 7984 28.90 - 57.80: 570 57.80 - 86.70: 46 86.70 - 115.60: 3 115.60 - 144.50: 1 Dihedral angle restraints: 8604 sinusoidal: 3868 harmonic: 4736 Sorted by residual: dihedral pdb=" C ASP B 376 " pdb=" N ASP B 376 " pdb=" CA ASP B 376 " pdb=" CB ASP B 376 " ideal model delta harmonic sigma weight residual -122.60 -135.45 12.85 0 2.50e+00 1.60e-01 2.64e+01 dihedral pdb=" N ASP B 376 " pdb=" C ASP B 376 " pdb=" CA ASP B 376 " pdb=" CB ASP B 376 " ideal model delta harmonic sigma weight residual 122.80 133.54 -10.74 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" C4' DG F 34 " pdb=" C3' DG F 34 " pdb=" O3' DG F 34 " pdb=" P DT F 35 " ideal model delta sinusoidal sigma weight residual 220.00 75.50 144.50 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 8601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2128 0.079 - 0.159: 160 0.159 - 0.238: 5 0.238 - 0.318: 0 0.318 - 0.397: 1 Chirality restraints: 2294 Sorted by residual: chirality pdb=" CA ASP B 376 " pdb=" N ASP B 376 " pdb=" C ASP B 376 " pdb=" CB ASP B 376 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C3' ADP D1101 " pdb=" C2' ADP D1101 " pdb=" C4' ADP D1101 " pdb=" O3' ADP D1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ASP A 85 " pdb=" N ASP A 85 " pdb=" C ASP A 85 " pdb=" CB ASP A 85 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 2291 not shown) Planarity restraints: 2364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 895 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C PHE D 895 " -0.034 2.00e-02 2.50e+03 pdb=" O PHE D 895 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG D 896 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C1034 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C ASN C1034 " 0.029 2.00e-02 2.50e+03 pdb=" O ASN C1034 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY C1035 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 87 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C VAL D 87 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL D 87 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS D 88 " 0.009 2.00e-02 2.50e+03 ... (remaining 2361 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 20 2.25 - 2.92: 5576 2.92 - 3.58: 21330 3.58 - 4.24: 32084 4.24 - 4.90: 52751 Nonbonded interactions: 111761 Sorted by model distance: nonbonded pdb=" OD1 ASN A 83 " pdb="MN MN A 502 " model vdw 1.593 2.320 nonbonded pdb=" N ASN B 83 " pdb="MN MN B 502 " model vdw 2.004 2.400 nonbonded pdb=" OD1 ASP B 8 " pdb="MN MN B 501 " model vdw 2.006 2.320 nonbonded pdb=" OD1 ASN B 83 " pdb="MN MN B 502 " model vdw 2.023 2.320 nonbonded pdb=" CD2 HIS A 222 " pdb="MN MN A 502 " model vdw 2.051 2.540 ... (remaining 111756 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 105 or resid 109 through 137 or resid 151 throug \ h 188 or resid 205 through 342 or resid 354 through 395 or resid 501 through 502 \ )) selection = (chain 'B' and (resid 1 through 188 or resid 205 through 395 or resid 501 throug \ h 502)) } ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.28 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 6.700 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 44.550 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 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: 56.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 14463 Z= 0.213 Angle : 0.619 13.986 19861 Z= 0.316 Chirality : 0.040 0.397 2294 Planarity : 0.003 0.036 2364 Dihedral : 17.725 144.499 5524 Min Nonbonded Distance : 1.593 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.06 % 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: 0.73 (0.22), residues: 1611 helix: 1.67 (0.21), residues: 686 sheet: 0.15 (0.35), residues: 225 loop : -0.56 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 30 HIS 0.008 0.001 HIS D 56 PHE 0.013 0.001 PHE A 366 TYR 0.013 0.001 TYR B 63 ARG 0.004 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.546 Fit side-chains REVERT: C 1020 MET cc_start: 0.7360 (ttp) cc_final: 0.6408 (ttp) REVERT: D 13 SER cc_start: 0.8825 (t) cc_final: 0.8415 (p) REVERT: D 990 ASP cc_start: 0.7422 (p0) cc_final: 0.7161 (p0) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2060 time to fit residues: 48.3237 Evaluate side-chains 94 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 GLN C 864 GLN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN D 851 GLN ** D1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1027 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14463 Z= 0.283 Angle : 0.627 7.353 19861 Z= 0.316 Chirality : 0.041 0.168 2294 Planarity : 0.003 0.040 2364 Dihedral : 17.679 145.515 2417 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.00 % Allowed : 9.35 % Favored : 89.65 % 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: 0.73 (0.22), residues: 1611 helix: 1.62 (0.20), residues: 674 sheet: 0.13 (0.33), residues: 255 loop : -0.49 (0.26), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 30 HIS 0.008 0.001 HIS D 919 PHE 0.021 0.002 PHE C 147 TYR 0.021 0.002 TYR C 144 ARG 0.004 0.000 ARG D 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 1.483 Fit side-chains REVERT: C 188 MET cc_start: 0.7824 (tmm) cc_final: 0.7591 (tmm) REVERT: C 990 ASP cc_start: 0.6863 (t0) cc_final: 0.6648 (t0) outliers start: 14 outliers final: 12 residues processed: 105 average time/residue: 0.2143 time to fit residues: 36.2169 Evaluate side-chains 96 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 851 GLN Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 893 ASP Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 905 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 72.3815 > 50: distance: 17 - 24: 34.319 distance: 24 - 25: 39.479 distance: 25 - 26: 56.263 distance: 25 - 28: 69.420 distance: 26 - 27: 40.062 distance: 26 - 33: 40.552 distance: 28 - 29: 39.595 distance: 30 - 31: 39.479 distance: 30 - 32: 57.121 distance: 33 - 34: 34.897 distance: 34 - 35: 40.785 distance: 34 - 37: 14.905 distance: 35 - 41: 9.069 distance: 37 - 38: 16.475 distance: 38 - 39: 50.628 distance: 41 - 42: 9.578 distance: 42 - 43: 38.570 distance: 42 - 45: 35.904 distance: 43 - 44: 43.508 distance: 43 - 49: 56.696 distance: 45 - 46: 57.515 distance: 46 - 48: 39.926 distance: 49 - 50: 38.703 distance: 50 - 53: 53.746 distance: 51 - 58: 25.972 distance: 53 - 54: 39.833 distance: 55 - 56: 57.488 distance: 55 - 57: 38.862 distance: 58 - 59: 47.587 distance: 59 - 60: 3.420 distance: 60 - 61: 3.955 distance: 60 - 64: 20.363 distance: 62 - 63: 57.432 distance: 64 - 65: 44.194 distance: 65 - 66: 39.412 distance: 66 - 67: 41.422 distance: 67 - 102: 26.906 distance: 69 - 70: 40.880 distance: 73 - 74: 27.963 distance: 74 - 75: 34.243 distance: 74 - 77: 47.396 distance: 75 - 76: 10.364 distance: 75 - 82: 50.710 distance: 76 - 110: 32.979 distance: 77 - 78: 57.088 distance: 78 - 79: 24.741 distance: 79 - 80: 42.203 distance: 79 - 81: 15.048 distance: 83 - 84: 31.292 distance: 83 - 86: 56.712 distance: 84 - 85: 63.173 distance: 84 - 91: 7.317 distance: 85 - 118: 31.694 distance: 86 - 87: 20.342 distance: 87 - 88: 41.094 distance: 88 - 89: 32.830 distance: 88 - 90: 6.612 distance: 91 - 92: 42.387 distance: 92 - 93: 41.868 distance: 92 - 95: 16.103 distance: 93 - 102: 69.665 distance: 94 - 124: 30.778 distance: 95 - 96: 14.005 distance: 96 - 97: 68.021 distance: 98 - 99: 56.520 distance: 99 - 100: 54.170 distance: 99 - 101: 55.389 distance: 102 - 103: 40.454 distance: 103 - 104: 53.516 distance: 103 - 106: 39.168 distance: 104 - 105: 6.665 distance: 104 - 110: 31.703 distance: 105 - 132: 31.060 distance: 107 - 108: 56.490 distance: 107 - 109: 56.299