Starting phenix.real_space_refine on Wed Jan 22 00:32:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e8o_27945/01_2025/8e8o_27945.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e8o_27945/01_2025/8e8o_27945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e8o_27945/01_2025/8e8o_27945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e8o_27945/01_2025/8e8o_27945.map" model { file = "/net/cci-nas-00/data/ceres_data/8e8o_27945/01_2025/8e8o_27945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e8o_27945/01_2025/8e8o_27945.cif" } resolution = 2.77 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 92 5.16 5 C 11284 2.51 5 N 3040 2.21 5 O 3276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 17704 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4378 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 529} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 9.68, per 1000 atoms: 0.55 Number of scatterers: 17704 At special positions: 0 Unit cell: (132.08, 80.08, 134.16, 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 92 16.00 P 12 15.00 O 3276 8.00 N 3040 7.00 C 11284 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.67 Conformation dependent library (CDL) restraints added in 3.6 seconds 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4112 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 12 sheets defined 57.6% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.793A pdb=" N ASP A 4 " --> pdb=" O ARG A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 17 Processing helix chain 'A' and resid 18 through 26 Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 69 through 80 removed outlier: 3.818A pdb=" N ASP A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 91 through 99 removed outlier: 3.772A pdb=" N LEU A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.876A pdb=" N TRP A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 154 through 167 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 205 through 224 Processing helix chain 'A' and resid 235 through 246 Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.682A pdb=" N ALA A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 290 through 307 removed outlier: 3.523A pdb=" N GLY A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.954A pdb=" N MET A 340 " --> pdb=" O HIS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 removed outlier: 4.146A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 444 through 456 Processing helix chain 'A' and resid 461 through 476 removed outlier: 3.882A pdb=" N PHE A 465 " --> pdb=" O PRO A 461 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 476 " --> pdb=" O ILE A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 removed outlier: 3.537A pdb=" N GLN A 483 " --> pdb=" O GLN A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 492 through 511 removed outlier: 3.555A pdb=" N LYS A 503 " --> pdb=" O ARG A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 529 Processing helix chain 'B' and resid 1 through 6 removed outlier: 3.793A pdb=" N ASP B 4 " --> pdb=" O ARG B 1 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 18 through 26 Processing helix chain 'B' and resid 37 through 50 Processing helix chain 'B' and resid 54 through 69 Processing helix chain 'B' and resid 69 through 80 removed outlier: 3.818A pdb=" N ASP B 80 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 89 Proline residue: B 86 - end of helix Processing helix chain 'B' and resid 91 through 99 removed outlier: 3.772A pdb=" N LEU B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.876A pdb=" N TRP B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 154 through 167 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 205 through 224 Processing helix chain 'B' and resid 235 through 246 Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.682A pdb=" N ALA B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 290 through 307 removed outlier: 3.523A pdb=" N GLY B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 316 Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.954A pdb=" N MET B 340 " --> pdb=" O HIS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 removed outlier: 4.146A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 385 Processing helix chain 'B' and resid 403 through 411 Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 440 through 443 Processing helix chain 'B' and resid 444 through 456 Processing helix chain 'B' and resid 461 through 476 removed outlier: 3.882A pdb=" N PHE B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 476 " --> pdb=" O ILE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 removed outlier: 3.537A pdb=" N GLN B 483 " --> pdb=" O GLN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 492 through 511 removed outlier: 3.555A pdb=" N LYS B 503 " --> pdb=" O ARG B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'C' and resid 1 through 6 removed outlier: 3.793A pdb=" N ASP C 4 " --> pdb=" O ARG C 1 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 17 Processing helix chain 'C' and resid 18 through 26 Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.818A pdb=" N ASP C 80 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 91 through 99 removed outlier: 3.772A pdb=" N LEU C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.876A pdb=" N TRP C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 154 through 167 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 205 through 224 Processing helix chain 'C' and resid 235 through 246 Processing helix chain 'C' and resid 257 through 276 removed outlier: 3.682A pdb=" N ALA C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 290 through 307 removed outlier: 3.523A pdb=" N GLY C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 316 Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.954A pdb=" N MET C 340 " --> pdb=" O HIS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 358 removed outlier: 4.146A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 385 Processing helix chain 'C' and resid 403 through 411 Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 440 through 443 Processing helix chain 'C' and resid 444 through 456 Processing helix chain 'C' and resid 461 through 476 removed outlier: 3.882A pdb=" N PHE C 465 " --> pdb=" O PRO C 461 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 476 " --> pdb=" O ILE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 483 removed outlier: 3.537A pdb=" N GLN C 483 " --> pdb=" O GLN C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 492 through 511 removed outlier: 3.555A pdb=" N LYS C 503 " --> pdb=" O ARG C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 529 Processing helix chain 'D' and resid 1 through 6 removed outlier: 3.793A pdb=" N ASP D 4 " --> pdb=" O ARG D 1 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 17 Processing helix chain 'D' and resid 18 through 26 Processing helix chain 'D' and resid 37 through 50 Processing helix chain 'D' and resid 54 through 69 Processing helix chain 'D' and resid 69 through 80 removed outlier: 3.818A pdb=" N ASP D 80 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 89 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 91 through 99 removed outlier: 3.772A pdb=" N LEU D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 104 Processing helix chain 'D' and resid 115 through 117 No H-bonds generated for 'chain 'D' and resid 115 through 117' Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.876A pdb=" N TRP D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 154 through 167 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 205 through 224 Processing helix chain 'D' and resid 235 through 246 Processing helix chain 'D' and resid 257 through 276 removed outlier: 3.682A pdb=" N ALA D 261 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 Processing helix chain 'D' and resid 290 through 307 removed outlier: 3.523A pdb=" N GLY D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 316 Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.954A pdb=" N MET D 340 " --> pdb=" O HIS D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 358 removed outlier: 4.146A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 385 Processing helix chain 'D' and resid 403 through 411 Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 440 through 443 Processing helix chain 'D' and resid 444 through 456 Processing helix chain 'D' and resid 461 through 476 removed outlier: 3.882A pdb=" N PHE D 465 " --> pdb=" O PRO D 461 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 476 " --> pdb=" O ILE D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 483 removed outlier: 3.537A pdb=" N GLN D 483 " --> pdb=" O GLN D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 492 through 511 removed outlier: 3.555A pdb=" N LYS D 503 " --> pdb=" O ARG D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 529 Processing sheet with id=AA1, first strand: chain 'A' and resid 110 through 113 removed outlier: 6.797A pdb=" N ALA A 134 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL A 178 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL A 136 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU A 180 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR A 138 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 135 " --> pdb=" O GLN A 230 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU A 232 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A 137 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 318 through 320 removed outlier: 6.259A pdb=" N VAL A 285 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY A 437 " --> pdb=" O PHE A 417 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 426 through 427 Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 113 removed outlier: 6.797A pdb=" N ALA B 134 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL B 178 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 136 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU B 180 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR B 138 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL B 135 " --> pdb=" O GLN B 230 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU B 232 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 137 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.259A pdb=" N VAL B 285 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY B 437 " --> pdb=" O PHE B 417 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 426 through 427 Processing sheet with id=AA7, first strand: chain 'C' and resid 110 through 113 removed outlier: 6.797A pdb=" N ALA C 134 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL C 178 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL C 136 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU C 180 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR C 138 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL C 135 " --> pdb=" O GLN C 230 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU C 232 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL C 137 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 318 through 320 removed outlier: 6.259A pdb=" N VAL C 285 " --> pdb=" O ILE C 364 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY C 437 " --> pdb=" O PHE C 417 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 426 through 427 Processing sheet with id=AB1, first strand: chain 'D' and resid 110 through 113 removed outlier: 6.797A pdb=" N ALA D 134 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL D 178 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL D 136 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU D 180 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR D 138 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL D 135 " --> pdb=" O GLN D 230 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU D 232 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL D 137 " --> pdb=" O GLU D 232 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.259A pdb=" N VAL D 285 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY D 437 " --> pdb=" O PHE D 417 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 426 through 427 788 hydrogen bonds defined for protein. 2232 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: 5.78 Time building geometry restraints manager: 6.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4972 1.33 - 1.45: 2836 1.45 - 1.57: 10124 1.57 - 1.68: 20 1.68 - 1.80: 148 Bond restraints: 18100 Sorted by residual: bond pdb=" O2B NAP D 601 " pdb=" P2B NAP D 601 " ideal model delta sigma weight residual 1.736 1.608 0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" O2B NAP B 601 " pdb=" P2B NAP B 601 " ideal model delta sigma weight residual 1.736 1.608 0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" O2B NAP C 601 " pdb=" P2B NAP C 601 " ideal model delta sigma weight residual 1.736 1.608 0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" O2B NAP A 601 " pdb=" P2B NAP A 601 " ideal model delta sigma weight residual 1.736 1.608 0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C4A NAP D 601 " pdb=" C5A NAP D 601 " ideal model delta sigma weight residual 1.385 1.465 -0.080 2.00e-02 2.50e+03 1.62e+01 ... (remaining 18095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 23812 1.81 - 3.61: 604 3.61 - 5.42: 104 5.42 - 7.22: 24 7.22 - 9.03: 16 Bond angle restraints: 24560 Sorted by residual: angle pdb=" N LYS C 324 " pdb=" CA LYS C 324 " pdb=" C LYS C 324 " ideal model delta sigma weight residual 114.75 109.88 4.87 1.26e+00 6.30e-01 1.50e+01 angle pdb=" N LYS B 324 " pdb=" CA LYS B 324 " pdb=" C LYS B 324 " ideal model delta sigma weight residual 114.75 109.88 4.87 1.26e+00 6.30e-01 1.50e+01 angle pdb=" N LYS D 324 " pdb=" CA LYS D 324 " pdb=" C LYS D 324 " ideal model delta sigma weight residual 114.75 109.88 4.87 1.26e+00 6.30e-01 1.50e+01 angle pdb=" N LYS A 324 " pdb=" CA LYS A 324 " pdb=" C LYS A 324 " ideal model delta sigma weight residual 114.75 109.88 4.87 1.26e+00 6.30e-01 1.50e+01 angle pdb=" C2A NAP B 601 " pdb=" N3A NAP B 601 " pdb=" C4A NAP B 601 " ideal model delta sigma weight residual 111.82 120.85 -9.03 3.00e+00 1.11e-01 9.05e+00 ... (remaining 24555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 9708 17.26 - 34.51: 1020 34.51 - 51.77: 236 51.77 - 69.03: 44 69.03 - 86.29: 8 Dihedral angle restraints: 11016 sinusoidal: 4592 harmonic: 6424 Sorted by residual: dihedral pdb=" CA GLY C 330 " pdb=" C GLY C 330 " pdb=" N ARG C 331 " pdb=" CA ARG C 331 " ideal model delta harmonic sigma weight residual 180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLY B 330 " pdb=" C GLY B 330 " pdb=" N ARG B 331 " pdb=" CA ARG B 331 " ideal model delta harmonic sigma weight residual -180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLY D 330 " pdb=" C GLY D 330 " pdb=" N ARG D 331 " pdb=" CA ARG D 331 " ideal model delta harmonic sigma weight residual -180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 11013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1656 0.039 - 0.079: 832 0.079 - 0.118: 212 0.118 - 0.158: 36 0.158 - 0.197: 8 Chirality restraints: 2744 Sorted by residual: chirality pdb=" C1B NAP A 601 " pdb=" C2B NAP A 601 " pdb=" N9A NAP A 601 " pdb=" O4B NAP A 601 " both_signs ideal model delta sigma weight residual False 2.31 2.51 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" C1B NAP C 601 " pdb=" C2B NAP C 601 " pdb=" N9A NAP C 601 " pdb=" O4B NAP C 601 " both_signs ideal model delta sigma weight residual False 2.31 2.51 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" C1B NAP B 601 " pdb=" C2B NAP B 601 " pdb=" N9A NAP B 601 " pdb=" O4B NAP B 601 " both_signs ideal model delta sigma weight residual False 2.31 2.51 -0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 2741 not shown) Planarity restraints: 3152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 345 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO D 346 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 346 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 346 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 345 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO B 346 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 346 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 346 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 345 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO C 346 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 346 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 346 " -0.018 5.00e-02 4.00e+02 ... (remaining 3149 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 480 2.70 - 3.25: 18532 3.25 - 3.80: 30784 3.80 - 4.35: 41384 4.35 - 4.90: 66248 Nonbonded interactions: 157428 Sorted by model distance: nonbonded pdb=" OG SER B 350 " pdb=" OE1 GLU B 353 " model vdw 2.148 3.040 nonbonded pdb=" OG SER A 350 " pdb=" OE1 GLU A 353 " model vdw 2.148 3.040 nonbonded pdb=" OG SER C 350 " pdb=" OE1 GLU C 353 " model vdw 2.148 3.040 nonbonded pdb=" OG SER D 350 " pdb=" OE1 GLU D 353 " model vdw 2.148 3.040 nonbonded pdb=" OG SER A 394 " pdb=" OE2 GLU A 401 " model vdw 2.186 3.040 ... (remaining 157423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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=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: 0.520 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: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 42.710 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 0.128 18100 Z= 0.489 Angle : 0.745 9.026 24560 Z= 0.382 Chirality : 0.047 0.197 2744 Planarity : 0.004 0.032 3152 Dihedral : 14.956 86.285 6904 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.16), residues: 2216 helix: -1.69 (0.14), residues: 1044 sheet: -2.52 (0.34), residues: 216 loop : -1.73 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 319 HIS 0.005 0.001 HIS A 200 PHE 0.017 0.002 PHE D 445 TYR 0.015 0.002 TYR D 74 ARG 0.005 0.001 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 1.5768 time to fit residues: 196.5180 Evaluate side-chains 76 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 7.9990 chunk 166 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 52 GLN A 66 GLN A 226 ASN A 282 HIS A 335 ASN A 385 HIS A 395 ASN A 474 GLN A 479 GLN A 554 GLN B 8 ASN B 52 GLN B 66 GLN B 226 ASN B 282 HIS B 335 ASN B 385 HIS B 395 ASN B 474 GLN B 479 GLN B 554 GLN C 8 ASN C 52 GLN C 66 GLN C 226 ASN C 282 HIS C 335 ASN C 385 HIS C 395 ASN C 474 GLN C 479 GLN C 554 GLN D 8 ASN D 52 GLN D 66 GLN D 226 ASN D 282 HIS D 335 ASN D 385 HIS D 395 ASN D 474 GLN D 479 GLN D 554 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.053976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.040535 restraints weight = 62243.252| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.46 r_work: 0.2544 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18100 Z= 0.184 Angle : 0.596 9.461 24560 Z= 0.299 Chirality : 0.042 0.154 2744 Planarity : 0.004 0.035 3152 Dihedral : 9.864 58.841 2696 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.85 % Allowed : 9.57 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.56 (0.17), residues: 2216 helix: -0.36 (0.15), residues: 1084 sheet: -1.72 (0.39), residues: 192 loop : -1.59 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 319 HIS 0.004 0.001 HIS A 200 PHE 0.015 0.001 PHE A 445 TYR 0.018 0.002 TYR A 517 ARG 0.003 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 1.989 Fit side-chains REVERT: A 196 ILE cc_start: 0.9260 (pt) cc_final: 0.8860 (pp) REVERT: B 196 ILE cc_start: 0.9253 (pt) cc_final: 0.8850 (pp) REVERT: C 196 ILE cc_start: 0.9258 (pt) cc_final: 0.8858 (pp) REVERT: D 196 ILE cc_start: 0.9259 (pt) cc_final: 0.8859 (pp) outliers start: 16 outliers final: 4 residues processed: 96 average time/residue: 1.1112 time to fit residues: 123.9365 Evaluate side-chains 80 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 147 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 140 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.051543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.038270 restraints weight = 64051.370| |-----------------------------------------------------------------------------| r_work (start): 0.2637 rms_B_bonded: 3.39 r_work: 0.2479 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 18100 Z= 0.365 Angle : 0.630 8.299 24560 Z= 0.310 Chirality : 0.044 0.155 2744 Planarity : 0.004 0.032 3152 Dihedral : 9.326 59.744 2696 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.28 % Allowed : 10.43 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.94 (0.17), residues: 2216 helix: 0.34 (0.16), residues: 1088 sheet: -1.68 (0.39), residues: 192 loop : -1.49 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 319 HIS 0.003 0.001 HIS C 115 PHE 0.014 0.001 PHE A 445 TYR 0.015 0.002 TYR D 517 ARG 0.003 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 2.025 Fit side-chains REVERT: A 15 MET cc_start: 0.9300 (mtm) cc_final: 0.8926 (mtm) REVERT: B 15 MET cc_start: 0.9299 (mtm) cc_final: 0.8922 (mtm) REVERT: C 15 MET cc_start: 0.9293 (mtm) cc_final: 0.8914 (mtm) REVERT: D 15 MET cc_start: 0.9297 (mtm) cc_final: 0.8918 (mtm) outliers start: 24 outliers final: 4 residues processed: 88 average time/residue: 1.1551 time to fit residues: 117.7780 Evaluate side-chains 76 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 188 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.052102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.038727 restraints weight = 61808.201| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 3.43 r_work: 0.2514 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18100 Z= 0.210 Angle : 0.565 9.064 24560 Z= 0.278 Chirality : 0.042 0.158 2744 Planarity : 0.003 0.032 3152 Dihedral : 9.131 59.414 2696 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.70 % Allowed : 11.28 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.53 (0.18), residues: 2216 helix: 0.63 (0.16), residues: 1096 sheet: -1.62 (0.39), residues: 192 loop : -1.20 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 319 HIS 0.002 0.001 HIS D 200 PHE 0.017 0.001 PHE A 445 TYR 0.013 0.001 TYR D 517 ARG 0.001 0.000 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 2.086 Fit side-chains REVERT: A 15 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8892 (mtm) REVERT: A 351 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9313 (tt) REVERT: B 15 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8880 (mtm) REVERT: B 351 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9313 (tt) REVERT: C 15 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8884 (mtm) REVERT: C 351 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9312 (tt) REVERT: D 15 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8879 (mtm) REVERT: D 351 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9310 (tt) outliers start: 32 outliers final: 4 residues processed: 96 average time/residue: 1.1770 time to fit residues: 131.3412 Evaluate side-chains 84 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 15 MET Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 98 optimal weight: 5.9990 chunk 219 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 205 optimal weight: 20.0000 chunk 151 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.050182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.037110 restraints weight = 64142.981| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 3.41 r_work: 0.2460 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18100 Z= 0.412 Angle : 0.647 10.094 24560 Z= 0.315 Chirality : 0.044 0.152 2744 Planarity : 0.004 0.030 3152 Dihedral : 9.099 59.515 2696 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.28 % Allowed : 13.19 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.46 (0.18), residues: 2216 helix: 0.75 (0.16), residues: 1088 sheet: -1.67 (0.39), residues: 192 loop : -1.21 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 546 HIS 0.003 0.001 HIS C 115 PHE 0.013 0.001 PHE B 445 TYR 0.015 0.002 TYR A 517 ARG 0.003 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 2.116 Fit side-chains REVERT: A 15 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.9015 (mtm) REVERT: B 15 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.9026 (mtm) REVERT: C 15 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.9025 (mtm) REVERT: D 15 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.9020 (mtm) outliers start: 24 outliers final: 4 residues processed: 88 average time/residue: 1.2231 time to fit residues: 124.7831 Evaluate side-chains 80 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 15 MET Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 29 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.051070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.038125 restraints weight = 63400.411| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 3.42 r_work: 0.2486 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18100 Z= 0.274 Angle : 0.593 10.346 24560 Z= 0.286 Chirality : 0.043 0.161 2744 Planarity : 0.003 0.031 3152 Dihedral : 9.111 59.588 2696 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.28 % Allowed : 13.83 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 (0.18), residues: 2216 helix: 0.84 (0.16), residues: 1096 sheet: -1.67 (0.39), residues: 192 loop : -1.10 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 319 HIS 0.002 0.001 HIS D 200 PHE 0.016 0.001 PHE D 445 TYR 0.012 0.001 TYR A 517 ARG 0.002 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 2.230 Fit side-chains REVERT: A 15 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8923 (mtm) REVERT: A 381 MET cc_start: 0.9638 (mtp) cc_final: 0.9437 (ttt) REVERT: B 15 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8920 (mtm) REVERT: B 381 MET cc_start: 0.9639 (mtp) cc_final: 0.9438 (ttt) REVERT: C 15 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8908 (mtm) REVERT: C 381 MET cc_start: 0.9640 (mtp) cc_final: 0.9439 (ttt) REVERT: D 15 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8918 (mtm) outliers start: 24 outliers final: 8 residues processed: 92 average time/residue: 1.4259 time to fit residues: 148.5262 Evaluate side-chains 84 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 15 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 143 optimal weight: 0.5980 chunk 198 optimal weight: 0.0470 chunk 75 optimal weight: 9.9990 chunk 201 optimal weight: 7.9990 overall best weight: 1.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.051971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.038890 restraints weight = 62570.618| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 3.46 r_work: 0.2515 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18100 Z= 0.186 Angle : 0.609 11.071 24560 Z= 0.291 Chirality : 0.042 0.151 2744 Planarity : 0.003 0.032 3152 Dihedral : 9.082 59.361 2696 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.06 % Allowed : 14.47 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.25 (0.18), residues: 2216 helix: 0.86 (0.16), residues: 1100 sheet: -1.54 (0.39), residues: 192 loop : -1.05 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 546 HIS 0.003 0.001 HIS B 200 PHE 0.016 0.001 PHE B 445 TYR 0.013 0.001 TYR D 208 ARG 0.002 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 2.060 Fit side-chains REVERT: A 15 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8881 (mtm) REVERT: B 15 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8868 (mtm) REVERT: C 15 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8864 (mtm) REVERT: D 15 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8872 (mtm) outliers start: 20 outliers final: 8 residues processed: 88 average time/residue: 1.2238 time to fit residues: 124.5109 Evaluate side-chains 84 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 15 MET Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 416 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.5514 > 50: distance: 39 - 49: 17.274 distance: 49 - 50: 8.955 distance: 50 - 51: 45.892 distance: 50 - 53: 31.386 distance: 51 - 52: 6.256 distance: 51 - 56: 52.079 distance: 56 - 57: 30.691 distance: 57 - 58: 27.953 distance: 57 - 60: 12.721 distance: 58 - 59: 14.399 distance: 58 - 63: 11.032 distance: 60 - 61: 19.690 distance: 61 - 62: 25.954 distance: 64 - 65: 17.544 distance: 64 - 67: 22.162 distance: 65 - 66: 7.207 distance: 65 - 70: 25.767 distance: 66 - 89: 32.043 distance: 67 - 68: 12.807 distance: 67 - 69: 5.722 distance: 71 - 72: 10.069 distance: 71 - 74: 12.968 distance: 72 - 73: 9.798 distance: 72 - 77: 10.059 distance: 73 - 94: 19.783 distance: 74 - 75: 13.269 distance: 74 - 76: 11.100 distance: 77 - 78: 6.540 distance: 78 - 79: 7.073 distance: 79 - 80: 29.762 distance: 79 - 81: 8.332 distance: 80 - 100: 19.877 distance: 81 - 82: 7.706 distance: 82 - 83: 7.517 distance: 82 - 85: 6.644 distance: 83 - 84: 11.295 distance: 83 - 89: 6.488 distance: 84 - 109: 21.365 distance: 85 - 86: 13.999 distance: 86 - 87: 27.813 distance: 86 - 88: 21.465 distance: 89 - 90: 3.950 distance: 90 - 91: 6.210 distance: 90 - 93: 8.226 distance: 91 - 92: 6.122 distance: 91 - 94: 5.722 distance: 94 - 95: 9.870 distance: 95 - 96: 11.833 distance: 95 - 98: 7.809 distance: 96 - 97: 17.455 distance: 96 - 100: 8.194 distance: 98 - 99: 19.416 distance: 100 - 101: 8.020 distance: 101 - 104: 6.430 distance: 102 - 103: 9.845 distance: 102 - 109: 7.517 distance: 104 - 105: 19.776 distance: 105 - 106: 21.706 distance: 106 - 107: 8.383 distance: 106 - 108: 24.691 distance: 109 - 110: 24.294 distance: 110 - 113: 18.205 distance: 111 - 112: 5.276 distance: 111 - 119: 8.676 distance: 112 - 138: 10.860 distance: 113 - 114: 14.521 distance: 114 - 115: 16.323 distance: 114 - 116: 21.275 distance: 115 - 117: 11.444 distance: 116 - 118: 13.015 distance: 117 - 118: 14.865